The new guidance comes as the school prepares to change its uniform policy.
Principal Andy Wood said requiring pupils to see the school's counsellor was to prepare students for the 'possible reactions from other kids'.
He told Stuff: 'In the meantime, as an interim measure we decided to ask girls who wished to wear the boys' shorts or pants to go via the counselling staff in order to check they had their parents' support, given the very small number of girls currently wearing pants.'
But one parent on social media was unhappy with the rules.
She argued that being forced to visit the counsellor could single pupils out and make them a target for bullying.
The school, which has 1870 students, is changing its uniform to incorporate a female version of the shorts and pants currently worn by male pupils.
The reform comes after feedback in 2018 calling for more options for female pupils.