Controversial legislation to regulate the use of embryos in scientific research looked likely to pass its first hurdle in the House of Commons last night, amid protests that Labour MPs would be forced into a whipped vote to ensure its progress.

Controversial legislation to regulate the use of embryos in scientific research passed its first hurdle in the House of Commons last night, amid protests that Labour MPs would be forced into a whipped vote to ensure its progress.

The government carried the day comfortably by 340 to 78, a majority of 262, in a vote on the broad principles of the Human Fertilisation and Embryology Bill that will allow the creation of hybrid or "admixed" embryos, which scientists hope will lead to developments in the treatment of conditions such as Alzheimer's and Parkinson's.

Nine Labour back benchers voted against the bill, among them Tom Clarke, MP for Coatbridge, Chryston and Bellshill.

Opening the second reading debate, Health Secretary Alan Johnson said the bill would bring this "new and exciting development" within a "strict legal and ethical framework".

The debate in the Commons exposed some of the deep divisions among MPs on the ethics of scientific research and several Labour MPs are expected to vote against some clauses in the committee stage which begins next week.

Some Catholic MPs and three government ministers oppose measures in the bill which scientists say are vital to improving fertility and the treatment of genetic conditions.

When the bill is considered in detail, Labour MPs will be allowed free votes on three issues - hybrid embryos, the creation of "saviour siblings" and preventing fertility clinics from refusing treatment to single women or lesbians.

Mr Johnson 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."

Fierce clashes are also expected next week when pro-life campaigners attempt to add amendments to lower the abortion time limit. Conservative leader David Cameron has said he would support lowering the limit to 20 weeks from its current 24 weeks.

Mr Johnson said: "Parliament's objective has always been to support scientific advances that benefit patients and their families through a clear legal, moral and ethical framework."

The bill updates the Human Fertilisation and Embryology Act 1990. Senior Tory Kenneth Clarke, health secretary at that time, said, "every member of the House was given a free vote on all issues they perceived to be ethical at any stage".

The Conservatives and Liberal Democrats have free votes on all stages of the bill.

Geraldine Smith, Labour MP for Morecambe and Lunesdale, said she would be in the no lobby with several colleagues. She said: "I fully respect the government's position on this, but I think the government should respect the position of members who will vote against the government tonight and I do that with sorrow."

Mr Johnson said the bill would give same-sex couples, who have children through assisted conception, the same parenting rights as heterosexual couples, bringing this area of law into line with other anti-discrimination legislation.

Shadow health secretary Andrew Lansley said: "If members have ethical considerations which, in their view, prevail over any other considerations, they should be in a position to exercise their judgment."