An Answer to the Claim that the Petrine Primacy was a Doctrine Invented in the Middle Ages
It is standard fare in the apologetics of Protestants and Eastern Orthodox to assert that the doctrine of the primacy of the See of Rome was an invention of the Middle Ages. A corollary of this assertion is the belief that, in the patristic era, the bishops patriarchal sees all interacted basically as equals with no concept of a Roman primacy until the early medieval era. How can a Catholic answer these charges?
Most Christians are totally unaware that the historical evidence for the Petrine primacy is quite rock-solid (pun intended). Many would assume there are good arguments that can be made either way, particularly among the Eastern Orthodox. Of course, neither Protestants nor Eastern Orthodox have an 'official' view as to how the papacy fits in with the historical testimony, but they all agree the papacy is a serious doctrinal error that crept in over the centuries. The goal of this article is to show that none other than the earliest Ecumenical Councils indicate the Bishop of Rome was Supreme Head of the Church , and given this fact, both Protestants and Eastern Orthodox are ultimately forced to admit the Church fell into apostasy, since the papal primacy is testified to by an agreed upon historical Christian witness. All quotes in this article are from virtually undisputed primary historical sources.
Canon 6 of Nicaea
Everyone is aware of the Council of Nicaea, held in 325, and how it was renowned for not only being the First Ecumenical Council but also for its importance in stopping Arianism. A common belief is that this was a gathering of 318 bishops of equal standing (i.e. no concept of a Roman primacy) who's collective conciliar authority won the day. But this concept fails to understand the reality of the ecclesial structures then in place, in which there clearly was a hierarchy of bishops, with the Pope at the top. An important testimony to this comes from Canon 6 of this same council, which states:
"Let the ancient customs in Egypt, Libya and Pentapolis prevail, that the Bishop of Alexandria have jurisdiction in all these, since the like is customary for the Bishop of Rome also. Likewise in Antioch and the other provinces, let the Churches retain their privileges. And this is to be universally understood, that if any one be made bishop without the consent of the Metropolitan, the great Synod has declared that such a man ought not to be a bishop."
This teaches that as per "ancient custom," there have been three major Sees, each retaining certain jurisdictions. The main 'controversy' surrounding Canon 6 is whether it is envisioning a 'trio of Patriarchs' rather than a Primacy of the Bishop of Rome. Preferring the former interpretation are obviously the Protestants  and the Eastern Orthodox. While a quick reading seems to lend weight to the the former reading, a more careful second look reveals that is not the case. Informed Catholics throughout the ages have pointed to a few key details as to why any reading other than that of Papal Primacy doesn't work.
First of all, from a grammatical point of view, the Canon says nothing about a jurisdiction in reference to the Bishop of Rome. Thus, the idea that Alexandria governs Egypt and Libya, while the Bishop of Rome governs some "Roman" land like Italy is projected onto the Canon, effectively putting words into it's mouth. This does not prove the Roman primacy, but it does help to remind us that this Canon does not deny a Roman primacy either, since no "Roman territory" is explicitly mentioned.
Second, in terms of the Canon making a logical argument, an interpretation that renders the Canon something to the effect, "Let the Bishop of Alexandria rule Egypt since it is customary for the Bishop of Rome to rule Italy" is a non-sequitur fallacy. In other words, it's irrelevant if the Bishop of Rome governs Italy, since that says nothing about who should rule elsewhere and especially what land they should govern. The same can be said if it is taken to mean "since it is customary for the Bishop of Rome to be a Patriarch," which brings out the logical fallacy all the more. For a Council that just got done addressing one of the most pernicious heresies of all time, including using precise and deliberate language for the Creed, we should expect a far more reasonable argument in Canon 6 than what Protestants and Eastern Orthodox have to offer.
If Canon 6 excludes some kind of "territory of Italy" over which Rome has primacy, what is the correct interpretation? The Catholic interpretation understands the Canon as follows:
"Let the Bishop of Alexandria continue to govern Egypt, Libya, and Pentapolis, since assigning this jurisdiction is an ancient custom established by the Bishop of Rome and reiterated now by this Nicene Council."
All of the sudden, this Canon has some "teeth". The appeal of the Council is to an ancient custom, which surely must have originated on some solid basis (i.e. not accepted simply "because it's old"), and this basis is none other than the delegation of the Bishop of Rome. Without question, only the Catholic interpretation of this Canon satisfies the intellect and confirms the Faith, especially when we look at it in the context of the Canons of the councils immediately following Nicaea which sought to expound upon Canon 6.
Council of Constantinople Canons 2 & 3
The Second Ecumenical Council, held in 381 (55 years after Nicaea), gives further credence to the Catholic position on the Papacy. Here are Canon 2 and Canon 3 from this Council:
Canon 2: The bishops are not to go beyond their dioceses to churches lying outside of their bounds, nor bring confusion on the churches; but let the Bishop of Alexandria, according to the canons, alone administer the affairs of Egypt; and let the bishops of the East manage the East alone, the privileges of the Church in Antioch, which are mentioned in the canons of Nicaea, being preserved; and let the bishops of the Asian Diocese administer the Asian affairs only; and the Pontic bishops only Pontic matters; and the Thracian bishops only Thracian affairs. And let not bishops go beyond their dioceses for ordination or any other ecclesiastical ministrations, unless they be invited. And the aforesaid canon concerning dioceses being observed, it is evident that the synod of every province will administer the affairs of that particular province as was decreed at Nicaea. But the Churches of God in heathen nations must be governed according to the custom which has prevailed from the times of the Fathers.
Canon 3: The Bishop of Constantinople, however, shall have the prerogative of honor after the Bishop of Rome; because Constantinople is New Rome.
Notice that Canon 2 clearly references Canon 6 of Nicaea in regards to the jurisdiction and prerogatives of Alexandria and Antioch, yet no mention is made of an alleged "Patriarchate" or "jurisdiction of Italy" of the Bishop of Rome. This is quite odd if, in fact, Canon 6 was meant to be interpreted in the Eastern Orthodox and Protestant manner. But such makes perfect sense with the Catholic understanding of Canon 6. No jurisdiction of Italy is mentioned because one did not exist. If it did exist, surely it would have been mentioned, along with those of Pontus, Thrace, Antioch and Alexandria. While the Bishop of Rome is properly Bishop of the Roman Diocese, as Successor of Peter he also has a final jurisdiction over all the local churches as well.
And if that wasn't enough, Canon 3 says the Bishop of Rome is of first rank, and that Constantinople being "New Rome" is thus to receive second rank among all the Bishops. This is utterly absurd if, indeed, there was an equality among the bishops, particularly an equality among Rome, Alexandria, and Antioch (i.e. the alternate reading of Canon 6). This only makes sense if Rome truly was of first rank and that this was universally understood this whole time. In other words, Canon 3 establishes that everybody already agreed that Rome was ranked first; Canon 3 simply establishes that Constantinople would now comes second.
More problematic is that within Canon 3 we see the seeds of what would blossom into an all out attack on the Papacy, with the Patriarchate of Constantinople initiating a power-grab that would throw the Church into serious turmoil.  As will be shown shortly, Canon 3 was never accepted by the Pope, and for reasons most Protestants and Eastern Orthodox would not expect.
The Proceedings of the Council of Ephesus
The Third Ecumenical Council gathered in Ephesus in the year 431 and condemned the heretic Patriarch of Constantinople, Nestorius. Though none of its canons directly pertains to the main subject, the Acts of the Council were preserved, and they shed important light on the significance of the papacy in the eyes of the whole Church. For example, in Session III of the Council, the Pope's head representative stated the following:
"Philip the presbyter and legate of the Apostolic See said: "There is no doubt, and in fact it has been known in all ages, that the holy and most blessed Peter, prince and head of the Apostles, pillar of the faith, and foundation of the Catholic Church, received the keys of the kingdom from our Lord Jesus Christ, the Savior and Redeemer of the human race, and that to him was given the power of loosing and binding sins: who down even to to-day and forever both lives and judges in his successors. The holy and most blessed pope Clestine, according to due order, is his successor and holds his place, and us he sent to supply his place in this holy synod, which the most humane and Christian Emperors have commanded to assemble, bearing in mind and continually watching over the Catholic faith. For they both have kept and are now keeping intact the apostolic doctrine handed down to them from their most pious and humane grandfathers and fathers of holy memory down to the present time."
This kind of talk was not out of the ordinary to those in attendance at the Council since the Pope's authority was acknowledged by all. This sounds nothing like what Protestants or Eastern Orthodox would have us believe about the "true" status of the Bishop of Rome. But this raises yet another point against them: if such manifest heresy as the papal primacy was being espoused, then surely someone would have gotten up and objected. Surely after condemning the Patriarch of Constantinople (Nestorius), the Council would have turned around and condemned this "Papalist heresy" while they were at it. But what did St Cyril of Alexandria, champion of orthodoxy at the Council say following this "outburst" by Philip? Observe:
"Cyril, the bishop of Alexandria said: "The professions which have been made by [the Papal Legates] Arcadius and Projectus, the most holy and pious bishops, as also by Philip, the most religious presbyter of the Roman Church, stand manifest to the holy Synod. For they have made their profession in the place of the Apostolic See, and of the whole of the holy synod of the God-beloved and most holy bishops of the West. Wherefore let those things which were defined by the most holy [Pope] Celestine, the God-beloved bishop, be carried into effect, and the vote cast against Nestorius the heretic, by the holy Synod, which met in the metropolis of Ephesus be agreed to universally; for this purpose let there be added to the already prepared acts the proceedings of yesterday and today, and let them be shewn to their holiness, so that by their subscription according to custom, their canonical agreement with all of us may be manifest."
So even St Cyril himself accepted the Pope's authority without any qualms at all, and indeed he was simply acting according to the instructions Pope Celestine gave to him prior to the start of the Council. Notice how all of this continues to confirm what the prior two Ecumenical Councils indicated. When looking at doctrinal development, it behooves us to look at the former through the lens of what it developed into later. When we see how the papal authority was received and agreed upon in the days of St. Cyril, we can better understand the context in which to read statements like those found in Canon 6 of Nicaea and Canons 2 and 3 of Ephesus.
The Council of Chalcedon
About 20 years later, the Fourth Ecumenical Council assembled in Chalcedon (451), and it is here where the Patriarch of Constantinople begins to vehemently assert himself in his struggle to overturn the Apostolic and Conciliar Tradition regarding the Supremacy of the Bishop of Rome. The primary goal of this Council was to condemn a new form of Nestorianism, especially after a "Robber Council" a few years earlier attempted to overturn the Council of Ephesus Council by declaring the neo-Nestorianism to be orthodox.  At Chalcedon, Pope St Leo the Great was the one who drafted the main document, the Tome, and it was widely hailed by the bishops in attendance as masterful defense of orthodoxy. Session II of the Acts of the Council records:
"After the reading of the foregoing epistle, the most reverend bishops cried out: This is the faith of the fathers, this is the faith of the Apostles. So we all believe, thus the orthodox believe. Anathema to him who does not thus believe. Peter has spoken thus through Leo. So taught the Apostles. Piously and truly did Leo teach, so taught Cyril. Everlasting be the memory of Cyril. Leo and Cyril taught the same thing, anathema to him who does not so believe. This is the true faith."
The famous line "Peter has spoken through Leo" has been cause for much disagreement, particularly because Cyril is mentioned right along side him. But this is because St. Cyril had already taken care of this original form of this heresy in the prior Council, which was addressed above, and they're rightly giving credit where credit is due (which is always the Catholic practice).  This in no way takes away from the fact the Council saw Pope Leo filling the chair of St Peter, and this language is not an accident, and confirms the Catholic position. When it came time to excommunicate Dioscorus, the Papal Legates said the following in Session III:
"Wherefore the most holy and blessed Leo, archbishop of the great and elder Rome, through us, and through this present most holy synod together with the thrice blessed and all-glorious Peter the Apostle, who is the rock and foundation of the Catholic Church, and the foundation of the orthodox faith, hath stripped him of the episcopate, and hath alienated from him all hieratic worthiness. Therefore let this most holy and great synod sentence the before mentioned Dioscorus to the canonical penalties."
Again, we see clear evidence of the Pope's authority in guiding the council and a reference back to Leo as Peter, the "rock and foundation" of the Church. But even after all this (and remember, the Western Bishops weren't present), when the time came to propose and vote on canons, in one of the most pernicious acts in Church history, the Council approved the infamous Canon 28:
"Following in all things the decisions of the holy Fathers, and acknowledging the canon, which has been just read, of the One Hundred and Fifty Bishops beloved-of-God (who assembled in the imperial city of Constantinople, which is New Rome, in the time of the Emperor Theodosius of happy memory), we also do enact and decree the same things concerning the privileges of the most holy Church of Constantinople, which is New Rome. For the Fathers rightly granted privileges to the throne of old Rome, because it was the royal city. And the One Hundred and Fifty most religious Bishops, actuated by the same consideration, gave equal privileges to the most holy throne of New Rome, justly judging that the city which is honoued with the Sovereignty and the Senate, and enjoys equal privileges with the old imperial Rome, should in ecclesiastical matters also be magnified as she is, and rank next after her; so that, in the Pontic, the Asian, and the Thracian dioceses, the metropolitans only and such bishops also of the Dioceses aforesaid as are among the barbarians, should be ordained by the aforesaid most holy throne of the most holy Church of Constantinople; every metropolitan of the aforesaid dioceses, together with the bishops of his province, ordaining his own provincial bishops, as has been declared by the divine canons; but that, as has been above said, the metropolitans of the aforesaid Dioceses should be ordained by the archbishop of Constantinople, after the proper elections have been held according to custom and have been reported to him."
In this canon, the Council not only reaffirmed the bogus power grab of Canon 3 of the Council of Constantinople, but here the Council pushed Constantinople to "equal" standing with Rome, as well as new tracts of areas by which to exercise its new jurisdiction. Now when it is said "the Council" did this, it is not to mean it was done in honesty and openness, but rather deceit. It did this without consulting the West or the Pope, and the massive political sway Constantinople held pressured the East to comply and vote it through.
But the absurdity of all this is plain by the words of this Canon: the "logic" employed by this Canon was that Patriarchal authority and jurisdiction corresponds to a city's size and political sway rather than to being founded by an Apostle and recognized as such from the start (see End Note #3). Such is a perfect demonstration of what political pressure is capable of, but Catholics know secular powers never trump the powers of Christ and His Church.
Leo's Defense of Rome's Prerogatives
In response to this shameless power grab, Pope St Leo the Great responded very negatively in a series of Letters, and in these Letters we see a defense of Papal Primacy at it's finest. To begin, we quote from Leo's Epistle 98, which the Council of Chalcedon sent to Leo, praising him for stopping the heresy but conclude by asking him to approve Canon 28:
"And we further inform you that we have decided on other things also for the good management and stability of church matters, being persuaded that your holiness will accept and ratify them, when you are told. The long prevailing custom, which the holy Church of God at Constantinople had of ordaining metropolitans for the provinces of Asia, Pontus and Thrace, we have now ratified [Canon 28] by the votes of the Synod, not so much by way of conferring a privilege on the See of Constantinople as to provide for the good government of those cities...We have ratified also the canon [Canon 3] of the 150 holy Fathers who met at Constantinople...for we are persuaded that with your usual care for others you have often extended that Apostolic prestige which belongs to you, to the church in Constantinople also... Accordingly vouchsafe most holy and blessed father to accept as your own wish, and as conducing to good government the things which we have resolved on for the removal of all confusion and the confirmation of church order. For your holiness' delegates, the most pious bishops Paschasinus and Lucentius, and with them the right Godly presbyter Boniface, attempted vehemently to resist these decisions...
For we duly regarding our most devout and Christ loving Emperors, who delight therein, and the illustrious senate and, so to say, the whole imperial city, considered it opportune to use the meeting of this ecumenical Synod for the ratification of your honour, and confidently corroborated this decision as if it were initiated by you with your customary fostering zeal, knowing that every success of the children rebounds to the parent's glory. Accordingly, we entreat you, honor our decision by your assent, and as we have yielded to the head our agreement on things honorable, so may the head also fulfil for the children what is fitting. ... But that you may know that we have done nothing for favor or in hatred, but as being guided by the Divine Will, we have made known to you the whole scope of our proceedings to strengthen our position and to ratify and establish what we have done."
Does this sound like an early Church that saw the Pope as one bishop among many, or even subordinate to a Council? Not by their own admission! Here a letter from an Ecumenical Council is begging a Pope to ratify a decision, admitting without such ratification the decision would indeed be a dead letter and attack on Christ's Body. Notice how they admit the Papal Legates adamantly rejected this decision, so they beg Leo even more to ratify it. In response, Pope Leo sent back various Letters, one of which was Letter 104 which he wrote to the Emperor:
"Let the city of Constantinople have, as we desire, its high rank, and under the protection of God's right hand, long enjoy your clemency's rule. Yet things secular stand on a different basis from things divine: and there can be no sure building save on that rock which the Lord has laid for a foundation. He that covets what is not his due, loses what is his own. Let it be enough for Anatolius that by the aid of your piety and by my favor and approval he has obtained the bishopric of so great a city. Let him not disdain a city which is royal, though he cannot make it an Apostolic See; and let him on no account hope that he can rise by doing injury to others. For the privileges of the churches determined by the canons of the holy Fathers, and fixed by the decrees of the Nicene Synod, cannot be overthrown by any unscrupulous act, nor disturbed by any innovation."
With a swift and solid blow, Leo exposes and demolishes the devious and faulty attempt to turn Constantinople into anything more than an honorary bishopric. Leo goes right to the heart of the error by pointing out Constantinople's bishop is founded on secular and political power, which is a different and inferior foundation than what the Church is built upon. Moreover, he says Canon 28 effectively tramples upon Canon 6 of Nicaea, which Leo explicitly references here and which we've already seen confirms the papal primacy. As Leo says, Canon 28 is an "innovation," based on an power hungry appetite which knows no limits - rightly foreseeing that Rome would be next in the cross-hairs of Constantinople's schemes.
Leo continued to write various Letters to various church officials and the Emperor contesting this. Let us examine Letter 106, which Leo wrote to the devious Patriarch of Constantinople Anatolius:
"And so after the not irreproachable beginning of your ordination, after the consecration of the bishop of Antioch, which you claimed for yourself contrary to the regulations of the canons, I grieve, beloved, that you have fallen into this too, that you should try to break down the most sacred constitutions of the Nicene canons: as if this opportunity had expressly offered itself to you for the See of Alexandria to lose its privilege of second place, and the church of Antioch to forego its right to being third in dignity, in order that when these places had been subjected to your jurisdiction, all metropolitan bishops might be deprived of their proper honor. By which unheard of and never before attempted excesses you went so far beyond yourself as to drag into an occasion of self-seeking, and force connivance from that holy Synod [Chalcedon] which the zeal of our most Christian prince had convened, solely to extinguish heresy and to confirm the Catholic Faith: as if the unlawful wishes of a multitude could not be rejected, and that state of things which was truly ordained by the Holy Spirit in the canon of Nicæa could in any part be overruled by any one. Let no synodal councils flatter themselves upon the size of their assemblies, and let not any number of priests, however much larger, dare either to compare or to prefer themselves to those 318 bishops, seeing that the Synod of Nicæa is hallowed by God with such privilege, that whether by fewer or by more ecclesiastical judgments are supported, whatever is opposed to their authority is utterly destitute of all authority."
Here we see one of the clearest and official expositions of Canon 6 of Nicaea. And of course, Pope Leo is simply affirming what the Church has always held: this makes Canon 28 of Chalcedon a "conniving" and "self-seeking" power grab aimed at trampling upon the dignity and jurisdiction of Alexandria and Antioch, all in direct violation to Canon 6 of Nicaea. From this point on, with seedlings emerging as early as Canon 3, Constantinople and Rome would be in a power struggle that caused serious damage to the Church. This wicked and demonic scheme to attack the Papacy even played a major part in Constantinople and the Eastern Christians being invaded and concurred by the Muslim Turks, and subjected to persecution to this very day.
Read More: Infallibility and the Case of Pope Vigilius
 I am indebted to Fr James Loughlin's masterful article he wrote in 1880 in the American Catholic Quarterly Review titled The Sixth Nicene Canon and the Papacy (found in full Here). I will attempt to summarize his major arguments.
 Note the irony that either option refutes Protestantism on historical grounds, since neither option is compatible with Protestant ecclesiology.
 A reluctantly admitted and generally hushed historical fact of Eastern Orthodox history is that Constantinople did not have Apostolic Roots, meaning it was not founded by an Apostle like Rome, Alexandria and Antioch, and thus never held the authority that those others did. Instead, Constantinople was a purely political concoction, which became the main metroplis of the Roman Empire after the emperor Constantine established it in the middle of the fourth century. This reality causes the Eastern Orthodox to cringe inside, because after all their hype for being ancient and orthodox, their leading Patriarchate is ultimately an invention, and only rose to its prominence due to massive political pressure.
 The so called "Robber Council" was a name given by Pope Leo. It was called by the Emperor and attended by about 200 bishops, but since it was condemned by Leo, it never held any authority. As various Catholics have pointed out, the irony here is that Eastern Orthodox accept Leo's ruling (even using his term "Robber Council") and have no principled basis for why to reject it other than its rejection by the Pope. For the Easter Orthodox to say the Robber Council was to be rejected because it taught heresy (which it did) is to beg the question, since by all other criteria it was a valid ecumenical council, and the purpose of councils is to definitively declare the truth.
 In the Chacedonian "Definition of Faith," when the first three Ecumenical Councils were reaffirmed, the Definition says this about the Third Council, "...the holy synod formerly held in Ephesus, of which Celestine of Rome and Cyril of Alexandria, of holy memory, were the leaders, we do declare that the exposition of the right and blameless..."