"If it isn’t Roman Catholic then it’s not a proper Church, Pope tells Christians" was the provocative headline for a front-page article in the London Times last month. The Vatican had just released a brief but meaty document to clarify what it regarded as mistaken views on interfaith dialogue.

The reaction was predictable. Protestant spokesmen welcomed Vatican honesty while criticising its "lust for power". Comments from the pews came thick and fast. "The Babylonian mystery religion is live and well in Papal Rome," wrote a Canadian. It was "self-serving exclusivism by the Pope," according to a reader in Seattle and "offensive and insincere" in the eyes of a reader in Melbourne.

Is Pope Benedict trying to revive the almost forgotten days of a Cold War of bigotry and intolerance between Catholics and Protestants? A closer reading of the 16-page document suggests that this is not the case at all. Let me explain.

When I was brought up I was taught that when saying in the Creed: "I believe (…) in One, Holy, Catholic and Apostolic Church" I was saying that I believed that this Church exists and that it is to be found in "the Catholic Church", which we understood as identical to "the Roman Catholic Church". My world was made up of Catholics (members of this one Church) and Protestants (who might be very good but were not members of the Church). We prayed for their conversion and were very happy when we heard of people – of whom there were many – who had asked to join the Church.

After the Second Vatican Council, especially perhaps in its immediate aftermath, things became more complex. It became unfashionable in the Catholic media to promote conversions. The buzz word was "ecumenism", often presented as dialogue between Christian communities without any real search for unity. What was sought was understanding, perhaps especially on the part of us Catholics: we had to learn to see all the good things which Protestants had. I remember my surprise at hearing of a German theologian actively dissuading a Protestant from becoming a Catholic, on the theory that it was better for him to remain (at least for the time being) a Protestant.

In part this change was justified by a tiny change in wording in a document from the Second Vatican Council. Before 1964, Catholics used to say that the Church founded by Jesus Christ is the Catholic Church. After 1964, they said that it subsists in the Catholic Church. Tiny? Yes. Momentous? Most emphatically. Almost immediately the change was interpreted as a sign that the Catholic Church was retreating from its claim that it was the authentic heir of Christ's legacy of doctrine and morals.

This was not true. All of the post-Vatican II popes have constantly reaffirmed the unique status of the Catholic Church. Why then had the phrase "subsists in" been adopted if it gave rise to such widespread misinterpretations?

We have to remember that Vatican II aimed, among other things, to be a Council open to the world and also, therefore, to Christians of other denominations. Anyone with a minimum of intelligence must recognise that many elements of Christianity are clearly to be found outside the strict limits of the visible Roman Church. The Council decided that it was good to state this publicly. This decision opened the door to cordial dialogue with those other communions.

Has this been fruitful? I think the answer is Yes. It has helped Catholics to open up to the riches of the Orthodox Churches and also to a better realisation that many Protestants are in good faith, have a great appreciation for much of Christ’s teaching and share many things with Catholics. In my own case, I remember discovering that 17th Century Anglicans had made extensive use of the works of mystics like St Teresa and St John of the Cross. And practical advances, like being welcomed, as a priest, to Anglican cathedrals; the introduction of Catholics to Anglican and Methodist hymns; the beautiful words of the Church of England marriage rite, and so on. Non-Catholics, for their part, have become much more willing to recognise the Pope as a world spiritual leader.

But there is also a down side. Seeing the good in other denominations (a good thing) has often led Catholics to think "we are all much the same" (which may be true, inasmuch as we are all sinners; but the difference, for Catholics, is that they believe they belong to a Church which is holy in spite of being made up of sinners) and then to adopt less demanding ways of behaviour of some non-Catholics (infrequent attendance at Church; acceptance of divorce and abortion and so on.).

This is one reason why Pope Benedict has asked his theologians (as did Pope John Paul II before him) to reiterate that the teaching about the nature of the Catholic Church has not changed. The Pope sees this not as a "put down" to non-Catholic Christians, but a stimulus. We still believe wholeheartedly in the Church, and that Christ has not failed. His Church still is on earth; still subsists.

For Protestants (and indeed for Orthodox), if they come round to admitting that Rome is not Babylon but a force for good, it means that they have "out there" a group of people who still carry the banner of the true Church, and the world is not confined to Christians groping around for unity and wondering whether Christ’s foundation has managed to survive.

Some consequences of the formulation "subsists in" are that the term "Church" (which previously was used by the Roman Catholic Church almost exclusively as referring to herself) can now be used, in a narrower sense, of those portions of the Church (including those not in full communion with Rome) which retain the Apostolic succession (the episcopate and with all the powers deriving from it).

Although the document says that the denominations resulting from the Protestant reformation cannot be deemed Churches from the point of view of Catholic doctrine, it is simply stating a logical consequence of their respective doctrines. Their notion of "Church" is different from the Catholic notion. Catholics respectfully recognise that Protestants freely decided in the 16th Century that the Catholic notions of priesthood and of the visible Church had no Biblical justification.

Finally, could we have saved ourselves a lot of trouble by not getting involved in what some see as a hornet’s nest with the phrase "subsist in"? This is a tenable opinion. Pope Benedict himself is reported as saying this summer that back in the days of the Second Vatican Council the enthusiasm of those involved was such that they didn’t realise that, as well as all the positive things emerging from the Council documents, there would also be a good number of negative ones.

However, we should not underestimate the good that has come from the ecumenical contacts of the last 40 years. The trust that Catholics have in the Popes should surely lead them to the conclusion that the best course is to keep hold of all the advantages flowing from Vatican II while remembering that what was taught before it remains true today. The two are not opposed and can go ahead together.

Father Andrew Byrne is a Catholic priest in London

Father Andrew Byrne is chaplain at Grandpont House, a residence for students at the University of Oxford, in England.