The trend for single-sex toilets is driven by the wish to be more inclusive of children who identify as transgender and wish to use the same facilities as the opposite sex.
Doctors and politicians have called on schools to halt the move towards unisex toilets to prevent any further harm to female pupils.
GP Tessa Katz said holding in urine for prolonged periods on a regular basis could increase the risk of girls suffering urinary and bladder infections.
"The psychological effects of girls not feeling safe enough to use mixed-sex toilets is also concerning," Dr Katz said.
At the same time, the rise in gender-neutral toilets has sparked a backlash among parents, many of whom say they were not consulted before the change was made at their children's schools.
The latest row involves Deanesfield Primary School in South Ruislip, West London, where parents launched a petition last month against the introduction of unisex toilets.
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One angry mother, who has daughters aged four and eight at the school, said: "The cubicles were open at the bottom and top so older pupils can easily climb up the toilets and peer over."
Stephanie Davies-Arai, from the parent campaign group Transgender Trend, said schools were being misinformed by "trans activist" organisations that they were breaking equality laws if they did not make toilets unisex.
She said there were clear exemptions under the current equality laws that meant it was perfectly legal to have single-sex toilets.
A spokesman for Deanesfield said: "We will continue to support parents with any individual worries or concerns they have."
Tory MP David Davies, who has backed feminist claims that transgender rights are overriding those of women, said: "If girls are not comfortable sharing toilets with boys then schools should make provision for them, rather than saying girls have got a problem."