Transgender advocates want more publicly funded sex reassignment surgeries after a gap was revealed between the number of transgender teens and such surgeries.
The Government pays for four sex changes every two years but a national study of youth health has found several hundred secondary students are either transgender, or think they might be.
The Youth '12 survey questioned 8500 secondary school students from Northland to Southland.
A question about whether they were transgender or not was included - the first time the question has been asked on a national level, University of Auckland researchers say.
It showed 102 were sure they were transgender, and 212 were not sure of their gender.
Study lead author Dr TerryAnn Clark said the number was higher than she expected.
"We had no idea what the prevalence of transgender identifying youth was in our population.
"We were surprised - that was a little bit higher than we had expected."
The Ministry of Health funds four reassignment surgeries every two years. Three of those are male to female sex changes, which are carried out in New Zealand, while the fourth funded surgery - female to male - is done overseas.
A ministry spokesperson said it did not know how many other surgeries were done, as it did not have data on private operations.
Ms Clark said the gap between the number of surgeries and the number of transgender people needed to be looked at.
"Absolutely, considering that there are probably young people and adults out there who feel a huge mismatch between their gender, their physical body and their identity, and how distressing that is to them and their mental health," she said.
"We have to start saying that this group aren't invisible, that they need services and we're doing a really poor job addressing them."
Time to step up
Michelle Jane Andrews, from Auckland's Rainbow Youth organisation, helped with the study and said the Government needed to step up.
"The kind of budgetary concerns over that are again coming from the perception that 'well this is a minority, we don't need to give too much budget to this'.
"So I think research like this is critical because it shows the Ministry of Health, the people that really should be recognising this in the first place, this minority is bigger than you realise, you need to re-evaluate how to support these people, because they are real."
Researcher Dr Mathijs Lucassen said several other issues for transgender youth were identified, and the study offered a variety of recommendations.
"They're quite practical things in terms of school records reflecting the gender identity of the students, school uniforms being inclusive and gender affirming and practical things in terms of school changing rooms and toilets, and making those safe and accessible for transgender students."
Dr TerryAnn Clark said she believed there would be a range of responses from schools to the survey but she hoped all schools would take up the recommendations.