Walton High campus on Walnut Tree recently converted its single sex loos into gender neutral unisex.
It is understood was move was designed to cut down bullying and to be more inclusive to transgender students.
But some parents have complained, saying their children were avoiding using the loo all day because they were uncomfortable about sharing with the opposite sex.
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One mum said: “My daughter finds it really embarrassing. I can't understand why a school would do this. Several of us have complained to the school but they don't accept that it's a problem.”
Unisex loos in schools are becoming increasing popular up and down the country and are approved by the Department for Education as long as he privacy is ensured by having an adequate cubicle enclosure and a full height door.
Experts say single sex toilets can be a breeding ground for bullying in the school environment.
They were part of the design when Walton High's new Brooklands campus was built three years ago and recently the Walnut Tree campus decided to follow suit.
Head teacher Miss Michelle Currie has declined to comment to the Citizen.
But she wrote a letter to a concerned parent stating the unisex toilets had proved “very popular” with girls and boys of all ages when they were introduced at the Brooklands Campus.
The letter stated: “Students from Walton High who visited the campus were impressed by the layout of the toilets and asked whether something similar could be achieved at the Walton High campus.
“This was discussed with members of the Student Council, who were involved with the redesign of the toilets and chose the colour scheme.”
Miss Currie's letter dismissed the parent's claim that pupils felt uncomfortable about using the new toilets. It stated: “Feedback from students about the changed has been very positive. There is no reason for a menstruating girl to feel in any way uncomfortable as each cubicle is completely private and the same number of sanitary bins are available as before.”
The letter's final paragraph states firmly: “Parents who attend our Open mornings see that Walton High has unisex toilets. If this is not something they want for their child then there are other schools they can choose instead.”
One parent said: “I am shocked by this response.”