The most famous moral compass in Britain has got itself stuck on a risky and dangerous course. Gordon Brown’s determination to “whip” Labour MPs and ministers in votes on the controversial Human Fertilisation and Embryology Bill risks ministerial resignations and the biggest rebellion of this parliament. It may also confirm Mr Brown’s short administration as being irredeemably accident-prone.

The bill is an important and controversial one. It includes provisions for the use of animal-human hybrid embryos in experiments. Screening to create so-called saviour siblings, those with a tissue match to existing children who require a donation of stem cells, bone marrow or even organs, will be allowed.

Doctors will be permitted to screen embryos for disease or disability. The “need for a father” test, previously applied by fertility doctors when treating single women or lesbian couples, will be scrapped. Amendments to reduce the upper limit for abortions from 24 to 20 weeks and permit the use of artificial sperm or eggs will be considered.

Each of these issues creates a potential moral minefield. Cardinal Keith O’Brien, leader of the Scottish Catholics, has called for a free vote and in a sermon today will describe the bill as “monstrous”. Peter Smith, the Catholic Archbishop of Cardiff, has written to the prime minister warning that these issues go to the “sacredness of human life, its meaning and purpose”.

Many MPs and ministers, and not just Catholics, are uneasy. Most do not want to wreck the bill but they do want an opportunity to change aspects of it. And if anybody needed any confirmation that the government is going down the wrong track, this weekend’s intervention by Ben Bradshaw, the creepily loyalist and lightweight minister, seals it. He has accused religious critics of the bill as “intemperate and emotive”.

The government’s case is that the legislation governing embryos, last updated in 1990, has been overtaken by scientific progress. That has left a democratic deficit, with the Human Fertilisation and Embryology Authority, an unelected quango, effectively making the law on issues of deep ethical concern. So changes in the law were necessary, the bill that has been drawn up is the government’s and by convention governments do not allow their ministers and MPs free votes on their own bills.

It is true that the law needs updating, as everybody involved in the debate agrees. It is also the case that there is a convention to allow free votes on important questions of conscience and religion. There is a highly relevant precedent here. When the Conservative government introduced the bill that became the 1990 act, it allowed a free vote. Nobody’s views were steamrollered, parliament decided and the legislation was the better for it. Why Mr Brown did not choose to follow that precedent is a mystery.

The fact that he has allowed himself to get into this mess speaks volumes. “Events”, particularly in financial markets and the wider economy, are giving him a big enough headache and have sent Labour crashing in the polls. To encourage a revolt smacks of incompetence.

The Westminster village is full of talk of the prime minister having sharpened up the Downing Street operation by bringing in outsiders such as Stephen Carter, a former public relations executive, as his chief of strategy. There is little sign of it so far and Blairite former ministers such as Stephen Byers are using the bill as a stick with which to beat the government.

There are suggestions this weekend that the moral compass is wavering and that MPs and ministers who oppose individual clauses in the bill will be allowed to abstain quietly, as long as their actions do not prevent it becoming law. If that is a compromise, it is a ropey one. Anybody who opposes the bill on moral grounds will surely not be party to such a grubby deal. MPs and ministers should have a genuine free vote.