Family First says allowing schools to introduce gender neutral toilets for transgender students is sending a "harmful message" and causing confusion.

The lobby group is today publishing legal advice around incorporating transgender students into the school environment and its national director Bob McCoskrie believes schools are being bullied into policies instead of seeking guidance.

At least one Wellington college has installed gender neutral bathrooms, and another is planning to.

"Legal opinion says that legally schools don’t have to allow that which is good but at the same time they need to allow for special circumstances," he told TVNZ's Breakfast programme today.

"What this is about is safety for the whole school environment and parents are not expecting their young daughters to be getting a biology lesson in the school toilets with a boy who thinks he is a girl.

"It's a safety factor as well. If you have a young girl who perhaps comes from a history of abuse, and then have a boy come in who thinks he is a girl, that's harmful to her. You've got to consider both parties."

"We think it's a harmful message. To target these messages at schools at young and vulnerable people saying if you're not happy with yourself, you can change your sex, that's a dangerous message, it's causing harm and it's causing confusion.