It comes as Freedom of Information requests showed that a number of councils have not looked in-depth at the impact that the change in policy will have on schoolchildren.
The Herald reports that a campaigner, Jess Stewart, believed that the FOI results show councils have not thought through the implications of the changes.
Under the new guidelines, young people can compete in sports events for their identified gender, as well as use the changing facilities of that gender, and that teachers aren’t mandated to tell the pupils parents.
“They are obviously wanting to do the right thing which is great. But they’ve done it without considering girls,” Ms Stewart told the paper.
She added: “Girls are absolutely negatively affected by this. It is important to raise awareness of transgender children but putting a transgender girl in a changing room with 30 other girls isn’t proportionate.
“They should at least have looked at the possible fall out from putting a male-bodied person in changing rooms which are being used by 14, 15 and 16 year old girls.”
The Children’s Commissioner, Education Scotland, and the Scottish Government all said that they did not carry out research on how pupils would be affected by the move.
Ms Stewart added: “In the rush to be trans inclusive, has every single adult who approved this guidance booklet completely forgotten about the needs of girls? Do our girls mean so little nowadays to not even deserve the right of privacy?
“On one hand the media is reporting about the sharp increase of sexual harassment and assaults of girls within schools and on the other we are telling our girls they no longer have the right to set their own boundaries of who can be within their private spaces when vulnerable.”
The Christian Institute has announced that it will take legal action on the guidance.
A Scottish Government spokesperson said: “The guidance is not a Scottish Government publication, however we are supportive of this work, developed by LGBT Scotland, which we believe will reduce transgender discrimination.
“It is up to individual schools and local authorities to deliver relevant and engaging learning that best suits the needs of pupils.”