New guidelines on transgender pupils for primary and secondary schools in England and Wales have been criticised for “ignoring the rights of girls”.

The confidential draft document from the Equality and Human Rights Commission (EHRC), seen by The Sunday Times, is expected to be introduced in October.

It seeks to protect not only those who meet the legal definition of gender reassignment but children “who are simply exploring their gender identity”. It applies to pupils of all ages, with or without medical intervention.

In sensitive areas of day-to-day life, where pupils have traditionally been separated by sex, schools will either be required or advised to open up to those identifying as the same gender.

So pupils who choose to identify as another gender should be allowed to use the changing rooms of that gender. Girls who are uncomfortable with the presence of a transgender girl are advised to use a private changing room.

Trans girls should have personal, social and health education lessons, which include sex education, with girls. It would be “unlawful indirect discrimination because of gender reassignment” to place a trans girl with boys if the school divides the sexes for these classes

When it comes to sport, the guidelines set netball skirts and tracksuit bottoms as the uniform for all pupils, who should be free to pick from a single list of approved items. Trans pupils must not be excluded from participating in single-sex sports such as team training and physical education. It is good practice for all PE lessons to be made mixed-sex.

On school trips, schools can lawfully decide to place trans pupils in single-sex rooms if they identify with that gender. A policy that requires all pupils to use the facilities of the sex recorded for them at birth could amount to indirect discrimination against a trans pupil.

Tanya Carter, of the campaign group the Safe Schools Alliance, which includes parents, doctors and teachers, said the group was “appalled” by the leaked draft, which “ignores the rights of girls”.

She highlighted the case of sex education classes for girls, which must now be opened up to trans girls. “What use is it to that pupil to learn about periods or breast development? No one is asking the girls whether they would feel happy with a trans pupil in that group. The EHRC has not listened to the voices of the concerned parents and teachers who would have to deal with the fallout if these policies are put into practice.”

Teachers are expected to help erase any record of a trans pupil’s sex at birth, reissuing certificates in the new name. They should also “investigate concerns about repeated or deliberate use of a previous name or pronoun”.

Teachers are warned they would break the law if they failed to call transgender pupils by their new names and pronouns. The EHRC says pupils “do not have to follow a legal process to start using a new name at school”. Under-16s only need a court order or parental consent to change their name. If a school allows pupils to change their names for other reasons, then it would be guilty of direct discrimination if it declined to do so for reasons of gender.

There is no easy way out for schools that try to resist by bringing in a general policy of not changing pupils’ names. That “could amount to indirect gender reassignment unless it was justified”.

The watchdog’s decision to affirm a child’s self-identification worries Marcus Evans, who resigned this year as a governor of the Tavistock and Portman NHS Trust, the only NHS gender identity service for children.

Evans, a psychoanalyst, said: “If John comes along to school and says ‘I no longer want to be John, I want to be Jane’ then if you immediately go along with the idea, you have made John cease to exist. But you can’t get rid of your psychological mind. We have all got to live for better or worse with ourselves.”

He criticised the policy of forcing other pupils to go along with a classmate’s decision to change gender identity. “Somebody they know as a boy they have got to think of as a girl. The confusion moves from the person to the rest of the class.”

David Isaac, chairman of the EHRC, said: “There are strong views and the debate had become very polarised. We are consulting with teachers, parents and various pro trans and feminist groups.”

The EHRC said in a statement: “This document is a draft. This will be an important document for schools to help them support all children and meet their legal duties under the Equality Act.”