Mary McAleese believes while the Vatican is losing its argument on its teachings, some youngsters in Catholic schools are left battling an internal conflict.
She said the numbers of young men who have died by suicide in Ireland is galling, with gay men one of the most at risk groups.
"They are the victims, one, of homophobic bullying; they are also frankly highly conflicted,"
said Mrs McAleese, who is studying canon law in Rome after her 14-year term which ended in November.
She said the vast majority of children in Ireland went to Catholic schools, where they would have heard the church's attitude to homosexuality.
"They will have heard words like disorder, they may have heard the word evil used in relation to homosexual practice," said Mrs McAleese.
"And when they make the discovery, and it is a discovery and not a decision, when they make the discovery they are gay when they are 14, 15 and 16 an internal conflict of absolutely appalling proportions opens up. They may very well have heard their mothers, their fathers, their uncles, aunts, friends use dreadful language in relation to homosexuality and now they are driven into a space that is dark and bleak."
She warned that with more debate, and greater research, the Catholic Church "is going to become increasingly isolated in its attitude to homosexuality" and gay people's civil and human rights.
The former president met the Papal Nuncio Charles Brown, who represents Pope Benedict XVI in Ireland, shortly after Easter to specifically draw his attention to the issue.
But she fears the issue will not be tackled until the "omerta" or code of silence on the issue is broken.
She also said the child abuse scandals have left "a massive hallowing out of trust" in the church's Episcopal leadership, but she believes it lost its grip on society years before as it insisted on obedience in a world where people were becoming increasingly educated and had access to other opinion.
The former president, who has published a book entitled Quo Vadis: Collegiality In The Code Of Canon Law, also criticised the church for not drawing in the views and anxieties expressed by its faithful.
She said: "Take, for example, the issue of abuse and the way the bishops handled that," she told Pat Kenny on RTE.
"The internal damage done to community, to trust, could in many ways have been avoided had there been much better lines of communication up through the system. If the people had been talking to their bishops, if the bishops had been listening, if the bishops had been talking freely and openly to the centre and had the opportunity at the centre to make their voices heard, part of the problem that we have has come from silence and come from a failure to set up structures where information flowed freely always."