By Robert Pigott
BBC News religious affairs correspondent
Opponents of the proposal say children need a father figure
It is normally the emotive issue of abortion or the complexities of hybrid embryos that have raised the greatest passions in the debate over the Human Fertilisation and Embryology Bill.
But the Church of England has reserved its greatest ire for the decision of MPs to allow single women and lesbian couples to seek IVF treatment without having to consider the need for a father for their children.
Its verdict is stark.
"This vote sends a signal that fathers don't matter," it said.
"The Church holds that a child's right not to be deliberately deprived of having a father is greater than any 'right' to a child through IVF.
"We are extremely disappointed that the important role of fathers was not recognised in the bill, and that we now have a situation where the perceived 'right' to have a child trumps the right for a child to be given the best possible start in life."
In Parliament, there was a vigorous attempt, led by the (Roman Catholic) former Conservative leader Iain Duncan Smith, to have the bill amended on the basis that it was "common sense" to include a father in bringing up children.
The Church of England focuses on how children end up without a father.
"There is a huge difference between a child who finds themselves in a single-parent family through bereavement or breakdown of parental relationship, and those who find themselves in this situation by design, for which this bill allows."
By comparison the Church's official reaction to the defeat of several attempts to cut the limit for abortion of 24 weeks' gestation was mild.
A spokesman said that "abortion is used too freely", but added that "the upper limit should be considered sympathetically on the basis of medical advances".
The problem for the Church of England - a large organisation lacking strong top-down authority - is the wide range of strong views on abortion held by its members.
The Roman Catholic Church is able to take a strong public line. Its leader in England and Wales, Cardinal Cormac Murphy-O'Connor, said before the debate that the country as a whole was becoming aware that almost 200,000 abortions in Britain each year was "somehow very wrong".
The cardinal told BBC World Service's The Interview that he was very disappointed with the vote, and that it had left many people deeply concerned.
Part of his concern is over what the church believes is the wider trend towards moral relativism - the move by people to replace rigid concepts of absolute right and wrong with decisions about what is right or wrong for them at the time.
The Evangelical Alliance, which claims a million Christian members, warned that what it called "ethical boundaries" had been further eroded by the vote to allow research on hybrid human-animal embryos.
David Muir, the alliance's public policy executive director, said: "Just because science can do something doesn't mean that it should.
"The drive for human improvement must not be allowed to trump the need to protect against harm and it is worrying to note the prevalence today of uncertainty and inconsistency relating to where ethical boundaries should be drawn, or indeed whether there should be any ethical boundaries at all."
The voting on the Human Fertilisation and Embryology Bill will be seen as another step in the process of secularisation of British society, and many will welcome it as such.
But the churches claim that in making such decisions politicians are out of step with the majority of voters who, they say, can see the dangers in giving scientists greater licence for research on human embryos.
The Evangelical Alliance put it like this: "There is a growing disparity between what the scientists and politicians are promoting and the opinion of the general public, who are increasingly uncomfortable with a utilitarian approach to human life."