A member of the Association of Catholic Priests has criticised Archbishop Diarmuid Martin's decision to transfer three seminarians to Rome.
Fr Brendan Hoban said the National Seminary in Maynooth could be extremely damaged by the move.
He made the comments following allegations of gay sexual activity, the use of the dating app Grindr and other anonymous allegations of misconduct at the seminary.
The Archbishop said he made his decision to send the Dublin seminarians at Maynooth to study at the Irish College in Rome because he was "somewhat unhappy" about a growing atmosphere in Maynooth where anonymous allegations were being made accusing people of misconduct or accusing the faculty at Maynooth of not treating allegations correctly.
"I felt that the quarrelsome attitude of that kind was not the healthiest place for my students to be".
Speaking on RTÉ's Morning Ireland, Fr Hoban said he found the decision remarkable given that Dr Martin has said that students should be prepared [for the priesthood] in their own culture.
He said: "I think he's unfair to Maynooth, I think he will damage Maynooth by what he's doing."
He said there has been consistent criticism of St Patrick's College for being unorthodox or not traditional enough, but the real issue of vocations is not being addressed.
Fr Hoban said the Archbishop is transferring three students while Dublin has 99 parishes and over a million Catholics and only one diocesan priest aged under 40.
"It seems extraordinary that attention is being given to moving deck chairs on the Titanic rather than getting to the issues that are important."
He added that the reality is that in a seminary there would always be a mixture of heterosexual and gay candidates.
"There will be, from time-to-time, incidents that maybe people would prefer that didn't happen. But they do happen, human nature being what it is."
However, he said in the overall picture nothing had been substantially proven as to what was happening in the seminary.
Fr Hoban said that in 2011 Cardinal Timothy Dolan was sent to Maynooth to investigate two things; the orthodoxy of the theology and allegations of gay sexual activity.
He said Cardinal Dolan said in his report that there was no evidence to support those allegations.
Fr Hoban said the association has no issue with seminaries being reformed, adding "they should be reformed but we don’t believe … that moving a few students here to Rome and making a big song and dance about it is any contribution to seminary reformation".
He said Maynooth needs reformation, as do all seminaries around the world, but "you need to reform the institution rather than take the ground from under it".
Separately, a former senior dean at St Patrick's College has said that the current controversy surrounding the college sounds and reads like a deja vu in many respects.
Fr Gerard McGinnity made complaints about the then vice president of the college Micheál Ledwith in the 1980s.
He said he was "shafted and deprived of his position" while the person he complained about was promoted.
Mr Ledwith resigned from the Presidency of Maynooth in 1994 and subsequently secured a teaching post in the US. He was laicised in 2005.
In 2002 the Catholic Church said Ledwith had made a private settlement with a minor who claimed he had sexually abused him.
Speaking on RTÉ's News at One, Fr McGinnity said whistleblowers should prepare for a "difficult passage".
He said he had doubts that things had changed in Maynooth over the last 30 years and he agreed with Dr Martin that a safe forum needed to be provided to enable seminarians with concerns to come forward.
In a statement, the Diocese of Ossary has maintained its "confidence" in Maynooth as an institution for students to study for the priesthood.
"The Diocese of Ossory continues to have confidence in Maynooth, as a place of formation for candidates for the priesthood, and in those charged with guiding it so that it can best serve the future of the church in Ireland," the statement said.
"No doubt Archbishop Martin and the other Trustees will continue to work to ensure that it models the best possible formation for the priests of tomorrow.
"We are hopeful to have a candidate for the priesthood for the coming academic year.
"As always we chose the location of formation according to the needs of the particular student and in this instance we intend to send him to Maynooth for his education and formation."
In a separate statement, the Bishop Waterford and Lismore Diocese said the diocese currently had four seminarians in total, one of whom was at Maynooth and he would be remaining there.
The statement said: "The Diocese of Waterford & Lismore have four seminarians at the moment - one in Maynooth who has completed a year and will continue his training there.
"The other three will begin their training in Rome, one in the Irish College, the other two in the Beda College.
"When making a decision as to the choice of seminary, I am guided by the particular formation needs and personal strengths of the individual concerned."