Justine Greening, who announced last summer she was in a homosexual relationship, said church practise should reflect "modern attitudes".
Speaking to Sky News, she said: "I think it's quite important we recognise that, for many churches, including the Church of England, that was something they were not yet willing to have in their churches."
Church of England legislation currently prevents clergy from marrying gay couples or blessing the marriages of same-sex couples.
Ms Greening, who is also the Education Secretary, went on to say: "I think it is important that the church in a way keeps up and is part of a modern country. I wouldn't prescribe to them how they should deal with that."
The matter of same-sex marriages has divided opinion within the Church of England, between those who are pushing for greater inclusion of same-sex couples and those who are resisting changes to church teaching they fear are unbiblical.
Rev Peter Ould, a commentator on Christianity and sexuality said people shouldn't giver her statement much weight, claiming that it's just her opinion.
He told Premier: "The truth of the matter is the Church of England under law is incapable of conducting same-sex weddings. Even if it wanted to there's a part of the Marriage (Same Sex Couples) Act forbids the Church of England from doing this."
He said Christians should respond to comments such as Greening's by deciding what their faith is worth to them.
He told Premier: "I don't really feel a time of great persecution is coming.... I think it may become more difficult and we need to stand for a biblical orthodox faith."
A Church of England spokesman was quoted by The Times as saying political leaders recognise the importance of the church determining its own position on the issue.
He said: "Parliament understood that it was an important aspect of religious freedom to allow Christian churches and other faiths to decide whether or not they could embrace same-sex marriage."
Listen to Rev Peter Ould speaking with Premier's Alex Williams: