Father Tony Flannery of the Redemptorist, a high profile Irish priest known for his views on issues such as female ordination and homosexuality, refused a Vatican edict to apologize this weekend for some of his positions in order to remain a priest in good standing.

According to the Irish Times, Fr Flannery wrote about why he feared excommunication and how signing the vatican document would violate his conscience.

There is “no question” of Fr Tony Flannery facing excommunication, senior Vatican sources have told The Irish Catholic, and they have insisted that the case hinges on whether or not the Redemptorist accepts the Church’s teaching on the nature of the priesthood.

During a press conference in Dublin at the weekend, Fr Flannery, 66, founder of the Association of Catholic Priests (ACP), a progressive organisation that represents more than 850 priests on the island of Ireland, said he was “threatened with excommunication from the Catholic Church for suggesting that, in the future, women might become priests and calling for this and other matters to be open for discussion.”

However, senior Vatican sources have indicated to The Irish Catholic that the Holy See has not threatened excommunication against Fr Flannery and the case is about the fundamental nature of the Church’s understanding of the priesthood.

Sources in the Roman Curia who spoke to The Irish Catholic this week claim that it is a 2010 contention by Fr Flannery that he no longer believed that “the priesthood as we currently have it in the Church originated with Jesus,” or that Jesus designated “a special group of his followers as priests,” that is problematic for the Congregation for the Doctrine of Faith (CDF).

“It is more likely that some time after Jesus, a select and privileged group within the community who had abrogated power and authority to themselves, interpreted the occasion of the Last Supper in a manner that suited their own agenda,” Fr Flannery writes.

According to The Irish Catholic, Vatican sources have indicated that the CDF want Fr Flannery to recant the statement and affirm that Christ instituted the Church with a permanent hierarchical structure and that bishops are divinely-established successors to to the apostles.

Fr Flannery says the Vatican warned him not to attend meetings of the Association of Catholic Priests. It is understood the Vatican is concerned that he was in a leadership role in an organisation that counts more than 1,000 priests as members.

The CDF is worried about the influence Fr Flannery’s published views on the nature of the priesthood might have on the members of that organisation.

Fr Flannery writes in the Irish Times, “I either put my name to a document that would be a lie, and would impugn my integrity and my conscience, or I face the reality of never again ministering as a priest.

“I have always believed in the church as the community of believers and as an essential element in promoting and nourishing the faith. I have enjoyed my years of preaching, the main work of Redemptorists, and never had any doubt that Christ’s message was one worth proclaiming.

“But to give up on freedom of thought, freedom of speech and most especially freedom of conscience is too high a price for me to pay to be allowed minister in today’s church.”

One Vatican source told the paper: “Here you have a priest, who is leading a priests’ association, apparently saying he doesn’t believe in the founding principles of the priesthood. That’s not good for the other members of this association.”

However, on the issue of excommunication, the source indicated that there is “no question” of Fr Flannery facing this ultimate penalty within the Church.

Even if he refuses to change his view, the sources indicated, Church law would not prescribe this severe punishment.