Earlier this month the Church ordered an inquiry into St Patrick's College in Maynooth, Co Kildare, amid accusations some trainees were using a gay dating app.
Catholic leaders said Ireland's leading priest training facility had an "unhealthy atmosphere" and the smart phone app Grindr was being used.
An inquiry will look at the "appropriate use of the internet and social media" by trainee clergymen.
The Catholic Archbishop of Dublin, Dr Diarmuid Martin, confirmed he was boycotting the seminary in the meantime.
Mary McAleese, herself a practicing Catholic, suggested the Church was too focused on homosexuality.
There are gay men "who are fine priests," she told the Irish Independent.
"We have the phenomenon of men in the priesthood who are both heterosexual and homosexual but the church hasn't been able to come to terms with the fact that there are going to be homosexuals in the priesthood, homosexuals who are fine priests," Mrs McAleese said.
"They haven't been able to come to terms with that because the teaching of my church, the Catholic Church, tells them that homosexuality is, of its nature, intrinsically disordered, those are the words of Pope Benedict and that homosexual acts are, in his words, evil.
"I am just worried that the Maynooth controversy seems to be concentrating on the wrong things. A seminary should be a place where people feel welcomed, not somewhere where they feel policed, after all, there are young people who haven't yet taken a vow of celibacy.
"They wanted to be reassured that neither place was, in their words, 'gay friendly', so they walked away happy that they were gay unfriendly, hostile to gay people - what sort of message does that send out to young men who are there who are gay, to priests who are gay?"
Founded in 1795, Maynooth College was once the largest seminary in the world.
It was built to train 500 trainee Catholic priests every year, but numbers have nosedived to just over 40 for the coming year with a fall-off in vocations.
Mrs McAleese, who was president from 1997 to 2011, has a gay son and campaigned for a yes vote in Ireland's same-sex marriage referendum.
