The 300-page document was drawn up the Equality and Human Rights Commission (EHRC) chaired by Baroness Falkner after the Supreme Court unanimously ruled that legally a woman should be defined by biological sex for the purposes of the Equality Act.
The EHRC has to provide practical advice to businesses and services about how this should work in practice.
Following the Supreme Court ruling in April, the EHRC produced interim guidance which said single-sex spaces should only be open to people of the same biological sex, otherwise they cease to be single-sex areas.
That would mean, for instance, that a trans woman – a biological male who identifies as a woman - would not be able to use women's toilets and changing rooms. Although the commission said they should offer transgender people suitable alternatives where possible.
The EHRC has said transgender people, who are also protected by equalities law, should be treated with dignity and respect.
The interim guidance has been withdrawn and an updated code of practice is awaiting approval. It can only gain legal force once it has been signed off by ministers and laid in Parliament for 40 days.
The new guidance, first reported by The Times, says that if there are concerns then decisions about access to spaces may need to be based on how someone looks.
It also says that if a transgender person is excluded from a space, the organisation should consider alternatives and that it would not be proportionate to leave the person without essential services, such as toilets.
The report says the guidance acknowledges that providing alternatives may not always be possible due to space constraints or cost and that determining someone's sex could be hindered by the fact there is "no type of official record or document in the UK which provides reliable evidence of sex".
Last month, Baroness Falkner urged the government to speed up its approval of the new code, warning that some organisations were operating under old guidance, which had become unlawful in the light of the court's decision.
Conservative shadow women and equalities minister Mims Davies has previously suggested Phillipson had chosen not to sign off the guidance because she did not want to damage her chances in the Labour Party deputy leadership election, which ended last month.
A source close to Phillipson described the claim as "utter nonsense".
Approving the guidance could be unpopular in some parts of the Labour Party.
During the deputy leadership contest, Lucy Powell, who eventually beat Phillipson to the job, said "I think we have got some of the language not right on this, and particularly around some of the guidance that's coming forward."
Last month, 32 Labour MPs wrote to the EHRC arguing that the interim guidance it issued in April, would "open the door to discrimination and harassment against trans people".
The interim guidance, which was withdrawn in October, is being challenged in the courts.
During the hearing in the High Court, the lawyer, representing the government, suggested the interim guidance may have been too simplistic and that access to spaces such as toilets could be judged on a case-by-case basis.