Ruth Kelly is a member of Opus Dei, a Roman Catholic organisation that follows a strict Vatican line on contraception, embryo research, cloning and abortion.

Ms Kelly, who has responsibility for a £1 billion research budget, opposed motions on embryo research in Parliament and is reported to have told Tony Blair that she could never support stem-cell research.

Robin Lovell-Badge, head of developmental genetics at the National Institute of Medical Research, told The Times Higher Education Supplement: “I have just been in the US and have seen how confused the situation is there. If someone as senior as Ruth Kelly is not going to favour stem-cell research we will end up with a similarly schizophrenic system in this country. It is very worrying.”

Nancy Rothwell, a Medical Research Council research professor and vice-president for research at Manchester University, said that it would worry her a great deal if ministers opposed stem-cell research.

“The views of ministers in the Department for Education and Skills (DfES) do matter as they are responsible for training the next generation of scientists. You can’t have a higher education policy that is at odds with the Government’s science policy,” she said.

The DfES refused to comment on Ms Kelly’s affiliation with Opus Dei. A spokeswoman said: “I am not going to discuss Ruth Kelly’s faith.”

But sources within the organisation confirmed that she attended meetings of the Roman Catholic organisation Opus Dei at Oxford with her brother Ronan Kelly. Dr Kelly, a hospital doctor currently doing research into herbal medicine in Singapore, is a “supernumerary” in Opus Dei, which makes him one of 500 British members and 84,000 members worldwide.

Unlike the movement portrayed in Dan Brown’s The Da Vinci Code, Opus Dei does not have its own monks but members include priests, bishops and at least one cardinal archbishop.

It has been controversial in the past due to its conservatism, secrecy and the practice of “mortification” where some members do penance by wearing a cilice or spiked bracelet around the top of the thigh, or by whipping themselves with a cat o’nine tails.

But the organisation is attempting to become more open about itself and to emphasise the life of holiness that its members attempt to lead.

There are four forms of membership or association. Most British members are supernumeraries, who are married but who make “commitments” to the aims of the organisation, or numeraries, who are celibate. The third form of full membership is as an associate, a person who is celibate but who lives out in the community and not in an Opus Dei centre.

Supporters can also become “co-operators”, individuals who pray regularly for the organisation and endorse its principles but who do not sign up to the commitments. Co-operators need not even be Catholic.

Among their duties, supernumeraries are encouraged to go to Mass daily, read the Gospel and say the Rosary. When Ms Kelly worked for The Guardian, former colleagues claimed, she attended Mass daily. Members also support the organisation financially.

Ms Kelly regularly attends meetings and other Opus Dei events, the organisation’s spokesman Jack Valero confirmed.

A senior Catholic source said: “There is no doubt whatsoever that Ruth Kelly is a fully paid-up member . . . on contraception, abortion, euthanasia and other issues such as stem-cell research, Ruth is very straight down the line.”

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