More than 100 leading academics have lined up with senior Labour figures in calling on Gordon Brown to grant a free vote in the Commons on embryo research.

In a letter to The Times today the 108 university professors – scientists, lawyers, philosophers and theologians – say that the Government should not erode the precedent of “conscience votes” on controversial bio-ethical legislation. They say that although they do not hold a common view on the proposals in the Human Fertilisation and Embryology Bill they all believe that votes on amendments to it should not be whipped.

Their views are shared by large numbers of Catholic MPs, including three Cabinet ministers.

The most controversial measures of the Bill include extending the permitted scope of embryo research to allow the creation of human-animal hybrid embryos. Another is to allow lesbian couples who have a child through fertility treatment to register themselves as joint legal parents. Some religious groups have attacked this as denying a child the right to a father, while supporters say that the issue is one of gay rights.

During the Commons proceedings there will also be an attempt to amend the Bill to change the abortion law by reducing the upper time limit for terminations.

The Bill has just passed the House of Lords, and Labour backbenchers have made clear that they will not accept any deal that allows Catholic ministers in the Cabinet with private concerns to absent themselves from key Commons votes on the measures.

Ruth Kelly, the Transport Secretary, Des Browne, the Defence and Scottish Secretary, and Paul Murphy, the Welsh Secretary, all face difficulties in supporting parts of the legislation.

But government whips, who include several Catholic MPs, among them Tommy McAvoy, their third in command, have advised Mr Brown that he could steer the legislation into law even if his MPs were not whipped to support it.

Such a move would be a marked change of tactics by the Government, which placed Labour peers on a three-line whip to support all votes but one on the Bill during its passage through the Lords. Tory peers had free votes and Lib Dem peers were whipped on clauses that were party policy.

Mr Brown is keen for Britain to entrench its position as a world centre for stem-cell research.

The talks are likely to delay further the introduction of the Bill to the Commons. It cleared the Lords in January.

Now that MPs have voted against a referendum on the Lisbon treaty, the Human Fertilisation and Embryology Bill will become one of the two most controversial measures before the Commons in this session, along with plans to extend the length of precharge detention for terrorism suspects to 42 days.

The Bill seeks to update the regulatory framework for fertility treatment and embryo research in line with advances in science. The legislation has prompted a more interventionist approach from the Catholic Church in England and Wales, which has lobbied Labour MPs to coordinate opposition to the Bill. The legislation is also about to start a debate on abortion laws, as antiabortion MPs will table amendments seeking to reduce the upper time limit for terminations while MPs who support abortion will seek to liberalise aspects of the law.

David Cameron gave impetus to the debate by declaring last week that he would support a move to lower the present upper time limit from 24 weeks.

Antiabortion MPs are pressing for parts of the committee stage of the Bill to be taken on the floor of the Commons and for a series of votes on options to reduce the upper time limit including to 13, 16 and 20 weeks.

The Commons Science and Technology Select Committee said last year that there was no evidence to support lowering the upper time limit and said that one doctor, not two as now, should authorise a termination.