Sixteen MPs defied the Labour whip yesterday to vote against the Human Fertilisation and Embryology Bill. Among them was Ruth Kelly, a Cabinet minister until the start of this month.

Tory and Lib Dem MPs had a free vote.

As a Roman Catholic Ms Kelly has been uncomfortable with the bill. It allows for the creation of human-animal embryos, from which stem cells can be harvested, but they must be destroyed after 14 days.

It will also allow lesbians and single heterosexual women equal access to IVF and fertility treatments and a lesbian or gay couple to be named on the birth certificate as the legal parents of their children.

Senior ministers are said to be furious that such a senior MP defied a three line whip and ignored the instructions of party managers.

Ms Kelly was in the chamber during the debate and appeared to have a speech prepared, but was not called to speak.

She announced last month her decision to leave the government and Parliament at the age of 40 and spend more time with her four young children.

She denied it was anything to do with the Embryology Bill when news of her departure emerged during the Labour party conference.

Ms Kelly’s appointment to the post of Minister for Equality in 2006 outraged gay equality activists.

A member of Opus Dei, she had never voted in favour of gay rights.

She was heavily criticised for delaying the implementation of the Sexual Orientation Regulations.

Ms Kelly has refused to say whether or not she personally regarded homosexuality as sinful.

A major row broke out in Cabinet in 2007 over plans to give Roman Catholic adoption agencies an opt-out from the Sexual Orientation Regulations, which outlaw discrimination on the grounds of sexual orientation when accessing goods and services.

Ms Kelly and former Prime Minister Tony Blair were said to support a faith-based exemption, but MPs and Cabinet colleagues defeated the idea.

Ms Kelly has been MP for Bolton West since 1997. She is standing down at the next election.

The Human Fertilisation and Embryoloy Bill passed the Commons last night by 355 to 129. It will now go to the Lords for a final reading before becoming law.

Other Labour rebels included former ministers Tom Clarke and Frank Field and Robert Flello, PPS to Communities Secretary Hazel Blears.