Gordon Brown was accused last night of forcing through measures to liberalise embryo research as one of his most senior colleagues refused to support him in the Commons.

Ruth Kelly, the Transport Secretary, made clear that she would not vote for the second reading of the Human Fertilisation and Embryology Bill. Although Ms Kelly has been given permission to stay away, a handful of Labour MPs are expected to abstain or vote against the Bill's second reading.

Gordon Brown has already been forced to grant a free vote when its most contentious clauses are discussed in detail next Monday and Tuesday. Now the Prime Minister is under growing pressure to allow MPs more time to debate measures that will allow the creation of hybrid human-animal embryos, the use of embryo-screening to produce “saviour siblings”, the need for a father in fertility treatment, and abortion law reform.

The Government was accused of “bringing Parliament into disrepute” for allowing just four three-hour debates on the reforms that have divided the Cabinet. Andrew Lansley, the Shadow Health Secretary, joined MPs on both sides of the debate in condemning the speed with which the new laws are being rushed through Parliament.

Evan Harris, the Liberal Democrat MP for Oxford West and Abingdon, plans to table an amendment that would allow embryos to be licensed purely for use in transplant therapy and not just for fertility treatment or medical research. This will have to be considered as part of the debate on saviour siblings, and he fears that there may now not be enough parliamentary time.

Dr Harris said: “It is vital that there is a free vote on saviour siblings, where I will support the Government, but it is also crucial that there is proper scrutiny of other aspects of that schedule, which deals with embryo research and testing, and I fear that in three hours we cannot do both.”

David Burrowes, Conservative MP for Enfield Southgate, who opposes the Bill, said: “Giving barely three hours to consider the principle of human admixed embryos, saviour siblings and whether we need a father ... surely that is bringing Parliament into disrepute.”

Ms Kelly's spokeswoman cited a private meeting on security with representatives from regional airports for her failure to vote. However, Des Browne, another leading Catholic member of the Cabinet, was expected to vote for the Bill last night. A senior government source rejected the calls for more time for debate, saying that Mr Brown was determined not to give further ground.

Other provisions included in the Bill include a ban on sex-selection for social reasons and the closure of loopholes that have left some fertility treatments unregulated. It also permits wider use of IVF records in medical research and allows surplus embryos to be used in medical training.

The three hours devoted to abortion will have to include debate over at least five possible options for change that are expected to be proposed. MPs who favour restricting abortion plan to table amendments that would fix the time limit at 13, 16, 18, 20 and 22 weeks. In the hybrid debate, amendments are likely on each of the four kinds of human-animal embryos covered by the Bill.

The government decision to allow Labour MPs a free vote only in these four debates, and not on the entire Bill's second or third readings, was also criticised.

Kenneth Clarke, Health Secretary at the time the exisiting 1990 embryology legislation was passed, said that it had allowed a completely free vote. “Every member of the House was given a free vote on all issues they perceived to be ethical,” he said.

Alan Johnson, the Health Secretary, said: “We do believe that some elements of this Bill require the same complete free vote for ministers and others. But the Bill itself, a flagship Bill of Government now building on a precedent that has gone on for 18 years, should be whipped at second and third reading.”

The father of Britain's first “saviour sibling” urged MPs to support a technology that has cured his son Charlie, now 9, of Diamond Blackfan anaemia, a life-threatening blood disorder.

Jayson Whitaker and his wife Michelle travelled to the United States in 2002 to use embryo-screening to conceive a child suitable to donate tissue to Charlie, as the procedure was not then allowed in Britain. Charlie received a successful umbilical cord blood transplant when his brother Jamie was born the next year.

“This legislation will allow people to make the same decision without forcing them to go abroad,” Mr Whitaker said. “We did an 8,000-mile round trip with a child who required ongoing medication and blood transfusions, and a two-year-old child. It was not a holiday. It was by no means pleasant. If the Bill gets passed, it's great news.”

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