Tabby Besley of InsideOUT, an advocacy group for rainbow students, said it was great that James Hargest College added another uniform option for girls - but maybe the school should rethink its process.
"We would not recommend that a student has to go to a guidance counsellor, or any staff member to wear a uniform of their choice.
"Inherently, it can 'other' a student - that they have to go and see a staff member to do that."
The idea of a female student seeing a guidance counsellor to talk through the potential reactions of other students, were they to wear pants or shorts, spoke to a wider issue, Besley said.
"To me, it shows that there's a wider problem in the school culture that they need to address. If they are experiencing negative reactions, like homophobic or transphobic bullying, then they need to address that.
"For people of all genders, it's common for most people to wear shorts in all sorts of environments. It shouldn't be a big deal."
InsideOUT offers practical resources and workshops help schools foster a safer environment for trans and gender-diverse youth, Besley said.
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Ministry of Education enablement and support deputy secretary Katrina Casey said school boards of trustees decided on uniform requirements.
"We do think that allowing students to choose from a range of flexible uniform options, regardless of their gender, is one way a school can support its culture of diversity and inclusiveness.
"We don't require schools to inform us however, in all cases we expect schools to communicate very clearly with parents when they are seeking to change existing rules about uniforms to make sure that the decision making process is collaborative."
If parents are concerned about school uniform requirements they should formally raise these with the board of trustees, Casey said.
Failing that, parents should contact their local Ministry of Education Office for advice.
It comes after Marian Catholic School in Hamilton decided girls were to continue wearing a pinafore, instead of culottes, last year after some parents complained that the more traditional uniform was hot and restrictive in the playground.
Fiordland College in Te Anau agreed that its students could wear "gender neutral" uniforms in 2019 after parents argued the old uniform, skirts for girls, was dated.
A Herald national survey of more than 500 schools in 2017 found that 79 per cent of schools that had uniforms said they offered gender-neutral options.