Parents have been outraged online after Carolside and Braidbar Primary Schools had the new facilities installed during the summer.
Urinals were taken out of the boys’ toilets with new floor-to-ceiling cubicles were built into the schools.
Currently, there are still separate male and female toilet blocks but headteachers have been told they are free to remove those boundaries.
Chris McGovern, chairman of the Campaign for Real Education hit out at the move.
He said: “East Renfrewshire Council and, indeed the Scottish government, appears to be so addicted to notions of political correctness that they are prepared to place children in danger of abuse or bullying.
“Girls, in particular, are likely to feel threatened and some may simply refuse to use the toilets. The council itself needs counselling and support in order to overcome its addiction.
“It needs to undergo a course of detoxification in order that common sense can be restored to its thinking. In the meantime, I fear for the well-being of the children.”
Independent councillor David Macdonald revealed that he has been contacted by numerous parents since the start of term last week.
He has written a letter to the council and said: “As you can probably understand, this has left some parents, worried, angry and upset, particularly for parents of girls approaching and going through puberty and those who need private spaces to deal with menstruation.
“On top of that. Let’s be frank here. Boys urinate on toilet seats whether by accident or on purpose.
“Are girls expected to enter a cubicle and be charged with having to wipe down a toilet seat with toilet paper to get rid of the urine and then be forced to make direct skin contact with the toilet seat when they sit down? I can’t imagine how incredibly unsanitary that situation will be, not to mention absolutely disgusting.
“It is my view that such a change cannot compromise the rights of boys and girls who are not transgender to go to the toilet in a gender-specific space.”
Parents were also critical online with Mary Russel branding the move “disgraceful” and Robert Cunningham insisting it is “political correctness gone mad”.
Others backed the move, however, Alyson Connell said: “How about we stop implying that girls should be afraid or repulsed by boys, raise our boys to not give them reason to be and start raising children who have respect for all.”
East Renfrewshire Council confirmed that moves to make toilets gender neutral were in response to Scottish Government guidance.
A spokesman said: “In line with guidance from the Scottish Government, to allow gender-neutral provision in our schools, where possible, future replacement toilets will now provide individual cubicles for pupils to use, giving complete privacy, with shared hand washing and drying facilities.
“Due to the fully enclosed cubicles, access to the toilets will no longer require a main door which has benefits including significantly reducing the likelihood of inappropriate behaviour in school toilets, increasing levels of privacy and creating safer spaces for children and young people to use.
“Individual schools will work with parents to establish the most appropriate way to operate these facilities, which are already commonplace in all new-build facilities.”