Diarmuid Martin has refused to send would-be priests to the training college
It has been claimed that the Holy See in Rome "has more gays per square inch than anywhere else in the entire world".
It comes as a split appears to be forming in the Catholic Church over an alleged 'gay subculture' at the seminary in Maynooth.
The Archbishop of Dublin Diarmuid Martin has refused to send would-be priests to the training college in Kildare, choosing to send trainees to study in Rome instead.
However the leader of the church, the Primate of All Ireland, Eamon Martin, has defended the college.
According to the Irish Independent, he is grateful to St Patrick's in Maynooth for the spiritual, human, pastoral and academic formation that he received there.
Meanwhile, the Association of Catholic Priests (ACP) says it regrets that the Maynooth seminary "has become a focus of unfair and unwarranted attention, highlighted by the decision of Archbishop Diarmuid Martin of Dublin to move Dublin diocesan students to the Irish College in Rome.
It says that while it is the prerogative of bishops to decide where students for the priesthood receive formation, it is also the responsibility of seminary authorities to "make sensible judgments on what candidates for priesthood are deemed suitable and to be allowed to make such decisions in good faith".
"It goes without saying that Irish priests should within reason be educated in Ireland.
"The damage this controversy will do to Maynooth is not in the best interest of the Irish Church," it adds.
Back in May, it was claimed that students in St Patrick's Maynooth were using the gay dating app Grindr in contravention of celibacy rules for priests.
Irish Times Rome correspondent Paddy Agnew says this issue is likely to be viewed as an internal Irish problem.
"I can tell you that the Holy See official reaction when it comes will be that this is a matter for the Irish bishops, for the bishops conference, for the Archbishop of Dublin, for the fellow bishops to deal with - it's not a matter Rome would be involved in," he told Newstalk Breakfast.
"It's not that they don't have their own problems of that nature in Rome," he said, referring to the previous case of a Polish monsignor who came out as gay last year.
"As somebody who went to a boys boarding school, as somebody who has two gay brothers, I'm not unaware of a gay sub-culture - and I can tell you the Holy See's probably got more gays per square inch than anywhere else in the entire world."