The cardinal said women who have unwanted pregnancies need more care
Cardinal Cormac Murphy O'Connor has said he was "deeply disappointed, but not depressed" by parliamentary support for the embryology bill.
The leader of the Roman Catholic Church in England and Wales told the BBC he was unsure whether MPs' votes reflected the unease felt by a lot of people.
MPs threw out bans on so-called saviour siblings and hybrid embryos, and rejected a cut to the abortion limit.
The cardinal repeated his call for a commission to comment on new science.
He said a national bioethics commission of scientists, health workers, religious leaders and ethicists should be established to comment on and research scientific advances.
Science does "wonderful things" but it cannot exist within a "moral vacuum", he told BBC Radio 4's Sunday programme.
"There's no doubt that a large number of people in this country are very uneasy about a lot of these matters that have been discussed this last week.
"They would like more time and better ways of reflecting on them in order to exhibit a truly moral conscience of what it is to be human," he added.
He stopped short of saying MPs were out of step with the rest of the country, but did question how well informed they were.
"We accept what Parliament decides but when Parliament decides on moral matters that does not necessarily mean they are totally moral.
"Parliamentarians often don't have enough time to consult and reflect."
Distress and concern
MPs rejected proposals to reduce the current upper time limit for abortions of 24 weeks, but the cardinal said that did not mean the matter was closed.
He said: "A vote in parliament is not the end of a matter of such deep concern and, to be absolutely frank, I'm not sure that the votes in parliament really reflect the distress and concern of so many people about the number of abortions in this country.
He said more was needed to be done to ensure there were fewer abortions and greater care was needed for women who have unwanted pregnancies.
"This means a conversion of the whole society so it's not just a matter of abortions, so it's not just a question of a vote in Parliament," he said.
He also stressed he would not be telling MPs how to vote ahead of the third reading of the human fertilisation and embryology bill.
"MPs must follow their conscience. That conscience must be informed. Catholic MPs must be informed by their Christian moral teaching. They then must make up their own mind," he said.