Phillipson, who is also the education secretary, said the government and the Labour Party were united in accepting the ruling that biological sex was the legal definition of a woman, despite widespread protests among activists at the decision.

Some senior ministers are also said to have expressed private unhappiness at the ruling. However, Phillipson told BBC Radio 4’s Today: “I speak for the government on this matter, and I can be crystal clear with you that we welcome the ruling.”

She praised the “clarity that the Supreme Court has delivered through the judgment that single-sex spaces are to be delivered on the basis of biological sex”.

Last week the Supreme Court ruled that the terms “woman” and “sex” in the Equality Act “refer to a biological woman and biological sex”, in a victory for campaigners who said that women’s rights were threatened by allowing biologically male trans women into female spaces such as toilets and changing rooms.

Phillipson, who appeared to be uncomfortable when repeatedly asked which bathroom a trans woman should use, said: “That should be on the basis of biological sex. That would apply right across the board to all single-sex provision.” She promised updated guidance from the Equality and Human Rights Commission on applying the judgment.

Last week Karin Smyth, the health minister, was unable to say which toilets a trans women should use. Phillipson’s comments suggest that the government has now hardened its position in light of the Supreme Court decision.

“The ruling was clear that provision and services should be accessed on the basis of biological sex,” Phillipson said, telling trans women: “You use the service that’s available on the basis of biological sex.”

Pubs and restaurants were urged, however, to ensure that there was a “safe and appropriate place for all people to use, including trans people”.

Phillipson said: “Many businesses have moved towards unisex provision, or separate cubicles that can be used by anyone … going to your local café, a local family café, chances are you’ll have one cubicle that’s self-contained, that can be used by anyone.”

The comments represent the latest shift of Labour’s thinking on gender after Starmer sought to shut down repeated controversies in which senior party figures were unable to say if women could have penises.

Last year Phillipson refused to say which toilets a trans woman should use but suggested that Labour’s plans to simplify the process for legally changing gender would clarify that those with a gender recognition certificate “would be using female toilets”.

After the Supreme Court’s ruling she suggested that she had always thought that female spaces should be able to exclude biological males, saying: “Before I was an MP, I managed a women’s refuge, so I know more than most how important it is that women — especially those who have experienced male violence, sexual violence and trauma — are able to access safe, therapeutic spaces.”

Phillipson is expected to make a statement to parliament on the ruling, saying that she wanted to “give MPs the chance to discuss this matter”. WhatsApp messages leaked over the weekend suggested that the Home Office minister Dame Angela Eagle and the culture minister Sir Chris Bryant were among senior Labour critics of the ruling.

Phillipson said that the judgment had far-reaching implications. “There are important questions around, for example, the use of toilets, around the use of changing facilities. But there are also profound questions that I think are even more important about, for example, hospital provision, rape crisis centres, women’s refuges, where you are talking about people often being in that provision on an accommodation basis for an extended period of time.

“I think it is important and welcome that the Supreme Court have put beyond doubt that providers can make sure that’s done on the basis of biological sex, because I do believe it is important that when … women have experienced abuse, male violence, that they are able to heal.”

Phillipson condemned “completely unacceptable” protests against the ruling after activists defaced statues in Parliament Square and carried placards suggesting that gender-critical feminists such as JK Rowling should be hanged.

Stephen Morgan, the minister for early education, told Sky News: “It’s completely unacceptable language to be used, and obviously any matters that break the law should be reported to the police, and hopefully police action is taken.”