The Secretary of State for Transport is to leave the government.

Sky News reports that Ruth Kelly has decided to stand down ahead of a reshuffle by the Prime Minister.

Labour party sources told PinkNews.co.uk that she is leaving over the Embryology Bill currently before Parliament, which has been vociferously opposed by the Roman Catholic Church.

However, Sky said that Ms Kelly, the mother of four children, is resigning for family reasons.

The BBC said she is “understood to be denying reports her decision had anything to do with her objections to the Embryology Bill.”

Ms Kelly is a devout Roman Catholic.

In May she voted in favour of an opposition amendment to the bill that would have retained a requirement on doctors to consider the need for a father when assessing women for fertility treatment.

The government argued that the consideration has been used to discriminate against lesbians and single women, and they defeated the amendment, which was proposed by former Tory leader Iain Duncan Smith.

The Daily Mail reports that Ms Kelly told friends she was ‘disgusted’ by the Prime Minister’s speech to the party conference today, in which he said that the UK should be leading scientific research.

The government won a vote on the Human Fertilisation and Embryology Bill in the Commons in May. It approved human-animal embryos for the harvesting of stem cells.

MPs were given a free vote on several clauses and three Roman Catholic cabinet ministers, Ms Kelly, Des Browne and Paul Murphy, voted against the government.

The Commons also approved the creation of so-called ‘saviour siblings’ and proposals that will allow lesbians and single heterosexual women equal access to IVF and fertility treatments.

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.

The revelation that she is to step down came just hours after Prime Minister Gordon Brown unveiled his plans for government in his well-received speech to the party conference in Manchester.

Sky News political correspondent Joey Jones said:

“It’s come as a huge shock… on the evening after what has been viewed as a successful day for Mr Brown, the news will be greeted by dismay from many Labour loyalists.

“She has four young children and wants to spend more time with them.

“She had decided this is the time to leave.

“The problem for Gordon Brown that his big day will be overshadowed by one of his key allies. The timing couldn’t be worse.”

A leading Roman Catholic leader in Scotland summed up the mood of many of the church’s adherents when he attacked the Labour party during Glasgow East by-election in July over its support for the Embryology Bill.

“Christian people have not changed. It is Labour that has broken its pack with Christian voters,” Joseph Devine, the Bishop of Motherwell, wrote in a letter to all MPs representing Scottish constituencies.

“What are we to do when our religion is attacked and our conscience outraged?

“When one considers the self-inflicted injuries this Labour Government has visited upon itself, one could be forgiven for thinking it had some kind of death wish.”

The Human Fertilisation and Embryology Bill is expected to complete its final parliamentary stages after the summer recess.

Ms Kelly has been MP for Bolton West since 1997.