In the House of Lords he said ministers should "see if there is anything that could be done to help reconcile the difficulties".
He was raising the case of after Revd Jeremy Pemberton from Nottinghamshire who lost his licence to be a priest when he entered into a gay marriage in April.
The local bishop told Revd Pemberton that his actions had gone against the teachings of the church.
Lord Fowler said: "Given that there are other clergymen at similar risk, will the minister as a matter of good will look at the position here and see if there is anything that could be done to help reconcile the difficulties?"
Baroness Northover, the UK government's Women and Equalities spokesperson replied: "My noble friend will know that the [gay] Marriage Bill sought to protect the position of religious organisations and that this is a matter for the Church of England. We hear what he says, and it is worth also bearing in mind that things can evolve. For example, it is good that we should soon see women bishops."
The Lord Bishop of Sheffield also spoke at the debate. He said: "My Lords, I thank the Minister for her affirmation that according to both the letter and the spirit of the legislation on same-sex marriage, it is for the Church of England and all faith communities to determine their doctrine and what is appropriate conduct for their clergy.
"Is the Minister aware that the recent guidelines of the House of Bishops state clearly that those who enter a same-sex marriage, together with children in their care, should be welcomed into the life of worshiping communities, and also that the Church of England is about to begin a two-year process of structured conversations to explore the changing attitudes to human sexuality and their implications for the life of the church and its disciplines?"