David Ford - who is attempting to introduce new legislation on allowing abortion in cases of fatal foetal abnormality - has claimed the Presbyterian Church has held different views on the matter.
The South Antrim MLA has submitted a Private Member's Bill in a bid to introduce reform.
If passed, women in Northern Ireland carrying a foetus unable to survive outside the womb would be allowed to have an abortion.
It is illegal in Northern Ireland for an abortion to be carried out on the grounds of such a diagnosis.
Mr Ford's move follows a previous failed attempt to change the law while he served as Justice Minister.
His church, however, has said "the taking of a child's life in general cases of fatal foetal abnormality cannot be justified".
It comes just days after the former Alliance leader was ousted as an elder at Second Donegore Presbyterian Church near Templepatrick over his support for same-sex marriage.
Asked if his attempts to legislate for abortion, in cases of fatal foetal abnormalities, would further create division between himself and his church, Mr Ford claimed the Presbyterian organisation had held differing views in the past on the matter.
"The position is quite clear that at different times there have been slightly different views expressed by a number of the Protestant churches," he told the BBC's Good Morning Ulster.
"The Catholic church was consistent in its response when the Department of justice carried out its consultation.
"Different views have come at different times from the Presbyterian Church and indeed also from the Methodist Church and Church of Ireland there has been an understanding around issues of fatal foetal abnormality."
On the church's view that there can be no justification for abortion, Mr Ford added: "I remember being told by a former moderator, that he did not think that was the view when he was moderator.
"So I am making the point that the view has changed at different times within the Presbyterian church."
He added: "I made a promise that I would seek to resolve the issue of women who are faced with the most traumatic circumstances possible.
"I am not seeking to force women who do not an abortion into having an abortion.
"But seeking to provide those women who feel that they can't carry to full term the opportunity to have an abortion.
"That is what I believe amounts to compassion."
The Presbyterian Church was asked to respond and referred us to a previous statement.
It restated its position that "human life begins at conception and that from that moment the human embryo should be treated in a manner in accordance with full human dignity".
And that at its general assembly in June, it called on the governments of Northern Ireland and the Republic to ensure that women received the best care possible around the birth period.