Archbishop of Dublin Diarmuid Martin has said he does not believe that the National Seminary in Maynooth, Co Kildare is the right environment for men to study to become priests.
He said he made the decision to move Dublin seminarians to study at the Irish College in Rome because he was "somewhat unhappy about an atmosphere that was growing" in Maynooth, saying that he felt it was not the healthiest place for his students to be.
Speaking on RTÉ's News At One, Dr Martin described as "quarrelsome" anonymous accusations being made on blogs.
There were allegations of gay sexual activity and other anonymous allegations of misconduct at the seminary.
Many allegations were made, he said, including accusations that students at Maynooth were using the dating app Grindr, and that authorities at the seminary were dismissing anyone who tried to make an allegation.
He said he had offered to provide an independent person for whistleblowers to approach, but the response to this offer was the publication of more anonymous letters.
He called the culture of anonymous letters "poisonous".
Authorities at Maynooth have to find a way to let people come forward with solid evidence to substantiate the allegations, he said.
"I offered, initially, to provide a person - totally independent person - and that they could go and in all confidence provide the evidence that they had - this is for whistleblowers. And the answer to that was simply more anonymous letters. That's not a healthy culture."
He said he would not tell any bishop not to send students to Maynooth but he would prefer his seminarians to be living in the reality of Dublin life where they would have the experience of pastoral work in a consistent way in a parish.
The Archbishop said that the seminary at Maynooth was very comfortable but he believed it needed some structural reform.
Meanwhile, the President of St Patrick's College in Maynooth has said that there is no investigation under way at the college, or complaints surrounding sexual harassment, misconduct or assault.
Monsignor Hugh Connolly told RTÉ's Drivetime that the college has always totally cooperated with statutory authorities and he urged people who have any fears or concerns to bring their complaints to the "civil authorities".
He said some of the anonymous correspondence "has been difficult" and has made for "a less than satisfactory atmosphere in which to conduct formation".
Msgr Connolly said that allegations surrounding a gay culture at the college or seminarians using gay dating apps certainly worries him and makes him "very unhappy".
He said he "has no concrete detail" of any such activity and part of the difficulty in dealing with complaints or rumours which are sourced anonymously is that they are difficult to process.
He said he expects all seminarians to live celibately at the college and "there can't be any compromise around that for a seminarian" and "that's non-negotiable".
He acknowledged that a new model of seminary, as suggested by Dr Martin, "would be very apt and has much merit".