Some Labour MPs warned they would defy the Government's decision to whip votes on the Human Fertilisation and Embryology Bill, despite having been offered a free vote on the most controversial issues.

Cabinet disagreements over the Bill emerged last night. Ruth Kelly, the Transport Secretary and a practising Roman Catholic, was granted permission to be absent from last night's vote on the Bill's second reading to attend meetings on airport security outside London. Aides made it clear she had "reservations" about parts of the Bill.

Des Browne, the Defence Secretary and also a Roman Catholic, made it clear that he would back the Bill in last night's vote, but said he would vote against plans to create hybrid embryos when Labour MPs have a free vote on the detailed measures later this month.

The Bill will allow the creation of hybrid embryos which scientists hope will lead to developments in the treatment of conditions such as Alzheimer's and Parkinson's. It will also allow the creation of "saviour siblings" – a genetic match for a sick brother or sister, and remove references to the need for a father when agreeing requests for fertility treatment.

Pro-life campaigners plan to use the Bill to press for the time limit on abortions to be cut from the current limit of 24 weeks to 22.

But ministers faced anger over their decision to insist that Labour MPs back the legislation at its second and third readings. They have agreed to allow Labour MPs a free vote on those controversial issues when the Bill reaches its later stages, but the Conservative and Liberal Democrat parties have offered their MPs free votes on all aspects of the legislation.

Alan Johnson, the Health Secretary, said the Bill would allow the "new and exciting development" of embryo research within a "strict legal and ethical framework". He 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."

But Geraldine Smith, the Labour MP for Morecambe and Lunesdale, became the first to defy the Government, warning: "I fully respect the Government's position on this, but I think equally the Government should respect the position of members who, on an issue of conscience, will end up voting against the Government tonight and I do that with sorrow. But I have to say I don't think it will damage the Government in any way – certainly not the way that former cabinet members writing books about the Government has damaged it."

Kenneth Clarke, the former Conservative chancellor and health secretary, criticised Labour's decision to whip their MPs for the second and third reading votes. He said that when the last set of legislation governing embryo research was passed, "every member of the House was given a free vote on all issues they perceived to be ethical at any stage – including ministers".

Andrew Lansley, the shadow Health Secretary, said the Government could and should have given MPs and peers a free vote. He said: "If members have ethical considerations which, in their view, prevail over any other considerations in a Bill, they should be in a position to exercise their conscience and judgement."