The cabinet is split over the bill, with three Catholic ministers - Ruth Kelly, Des Browne and Paul Murphy - and a few junior ministers all struggling to accept parts of it, to the private exasperation of some colleagues.
Brown now faces a choice between surrendering to demands for a free vote, which could see the bill defeated, or risking ministerial resignations on conscience grounds.
The Human Fertilization and Embryology Bill includes plans to create human hybrid embryos for research purposes. They would then be used to further medical research, potentially easing the suffering of millions.
Experts say this would give scientists the large number of embryos needed to make stem cells.But some quarters say using human-animal embryos for experiments would be ethically unacceptable.
Several senior members of the clergy, including Roman Catholic Cardinal Cormac Murphy-O'Connor, used their Easter sermons to condemn the plans and call for a free vote.
For his part, Health Secretary Alan Johnson played down reports of ministerial rebellion and a government compromise, saying there is no cabinet split.
He added that legislators will deal with this issue in the same way they deal with all sensitive legislative issues. Johnson said PM Brown made it plain three or four weeks ago that we will not be forcing people to vote against their conscience.
Supporters say the Human Fertilization and Embryology Bill will give scientists the large number of embryos they need to make stem cells to help find cures for a range of diseases.
Medical Research Council Chief Leszek Borysiewicz explained that scientists create inter-species hybrids by injecting human DNA into a hollowed-out animal egg cell.
The resulting embryo is 99.9 percent human and 0.1 percent animal.
Britain is one of the leading states for stem cell research, attracting scientists from around the world with a permissive environment that allows embryo studies within strict guidelines.
