Back in mediaeval times, the Catholic Church burnt non-believers at the stake. These day, punishment for those who challenge church doctrine is more subtle but equally effective, says gay priest Julian Ahern.

Yesterday Father Ahern faxed his resignation to Melbourne's Catholic leader, Archbishop George Pell. "In light of my personal and public love for the church, I guess it is the hardest decision I've ever made."

He explained yesterday why he had no choice but to quit. Since "coming out" in 1997, he was increasingly isolated by the church hierarchy and attempts to discuss the the issue of gay clergy with Archbishop Pell were fruitless.

First he lost his parish work, then his stipend was stopped - which left him without income. Since then he has survived on government sickness benefits, fighting depression brought on by the church's rejection of his sexuality.

"The archbishop has basically said I must accept the church's teaching in general, with the implied threat that I accept the doctrine against homosexuality in conscience. It rips my heart out how something that represents God can be basically irrational, if not mad," he said.

Father Ahern said he might be Australia's first openly gay priest to resign because of his fight against a doctrine that condems homosexuality as evil. "If the church is not listening to its clergy and the clergy don't have the courage to say who they are, then the whole church will fall apart."

In May the Vatican invited him to a conference on faith and learning. Now, as he looks at the photo of him at a mass with Pope John Paul, Father Ahern smiles wryly. "It's bizarre, how someone can welcome you on one hand and reject you at the same time."