Schools are being urged to offer "gender-neutral" uniform, toilet and changing room options under new guidelines from the secondary teachers' union.
The union, the Post Primary Teachers' Association (PPTA), says both boys and girls should be able to "choose from a range of shorts, trousers, skirts of different lengths and styles, with both tailored and non-tailored interchangeable shirts".
"It is important that access to specific uniform items is not limited on the basis of biological sex or perceived gender identity," the guidelines say.
They also urge schools to provide "individual toilet and shower units with lockable doors and floor-to-ceiling divisions" and "options for students to change and shower in privacy".
Although the guidelines are purely advisory, Principals' Federation president Whetu Cormick applauded the initiative.
"My view is that all kids should feel safe to be who they are culturally and in terms of their sexuality, because we know that if kids can be who they are in a whole range of areas they will achieve better," he said.
But the issue has become politically sensitive since President Trump reversed an Obama Administration measure that gave transgender students a right to use the bathrooms of their choice.
Avondale College biology teacher Shawn Cooper, who led the PPTA's Rainbow Taskforce which drew up the guidelines, said wearing skirts often put girls off physical activity.
Auckland University's Youth 2012 survey of secondary school students found that 68.5 per cent of boys, but only 56.5 per cent of girls, did more than 20 minutes of "vigorous activity" at least three times in the past week.
"We are hearing back from schools all around the country, and even in my own school girls inevitably are wearing skirts and a number of them do wear shorts underneath," he said.
"Certainly girls do talk about the fact I'm seeing boys out there playing rugby and in their skirts they feel restricted from doing the same amounts of physical activity."
Tabby Besley of InsideOUT, a support group for students, said Wellington Girls' and Wellington East Girls' Colleges adopted gender-neutral uniform policies last year and many schools had requested copies of her group's resource on Making Schools Safer for Trans and Gender Diverse Youth.
"InsideOUT believes things like providing gender neutral uniforms and toilets is an important step that all schools should be taking to ensure they acknowledge, include and support their trans students," she said.
InsideOUT co-chair Kate Aschoff and her friends campaigned successfully last year for Wellington East Girls' College to introduce shorts as a uniform option.
Aschoff, now 18, said her trans friends had to battle to wear pants, get their teachers to use the correct pronouns or have their name changed on report cards.
Proactively offering other uniform options and gender-neutral toilets could cut the drama out of what can already be an uncomfortable situation for a young trans person, she said.
"From a queer perspective, it's really important that they're acknowledging students' diversity in a space that's often gendered. Especially at a co-ed school, if you have to pick boys' or girls' uniform they're telling students to choose a box."
Forcing young people to decide whether to use a boys' or girls' bathroom tells them "you have to choose now, you have to know who you are", she said.
"If you have two bathrooms, going into one or the other is a political statement."
In New Zealand, the Family First lobby group has issued its own guidelines saying: "No child should be forced into an intimate setting - like a toilet block or a changing room - with another child of the opposite sex."
Its director Bob McCoskrie said the belief that gender identity could differ from biological sex, so that a person could be a "man trapped in a woman's body" or vice versa, was not supported by scientific evidence.
"Separate facilities reflect the fact that boys and girls have bodily differences; they are designed to protect privacy related to our bodies. We can figure that out - why can't the PPTA?" he said.
Heidi Hayward, principal of Dunedin North Intermediate, said she couldn't believe the reaction after her school allowed boys and girls to choose from five uniform options including shorts, long pants, culottes and a kilt.
"I have done an interview with the BBC in Russia, and with French TV," she said.
"That has been more alarming to me than anything. We had been doing it for a while before it hit the media."
She said she allowed children to choose any of the uniform options after three girls asked her in enrolment interviews in late 2015 whether they had to wear a skirt.
"I started thinking actually it was a bit embarrassing that I was saying yes, because if I was told I had to wear a skirt every day I'd be reading the Riot Act," she said.
She said no boys had actually chosen to wear skirts and only two girls wore shorts last year.