Parents have claimed their children have been told the wall had been removed to stop smoking, bullying and pupils skipping class and hiding in the toilets.
The high school is a voluntary aided academy for 11 to 17-year-olds, meaning it is not run by the local authority and is self-governed.
One parent said she thought the removal of the toilet wall was "absolutely disgusting".
She added: "They clearly haven't considered what girls past puberty have to deal with, so to have only one door for privacy without the added security of a room is terrible.
"There are classrooms opposite the toilets, there is even a camera facing them. For girls between the ages of 11-16 it's unacceptable."
Another parent, whose daughter is in Year 10, said the school did not tell her about the change to the toilet block and she is worried for her child.
She said: "My daughter told me all the girls feel as though they have no privacy and don't feel comfortable to use the toilet during school any more.
"I didn't know anything about the new toilets until she came home yesterday - she said she won't use them so if needs be I will say that she needs to go home at lunchtime to go to the toilet."
The mum said she understands that the boys' toilets are yet to be altered but soon will be.
She added: "I wouldn't like to use those toilets knowing people can see and judge you from their classroom or corridor.
"But I was unaware of the issue with bullying. Fortunately my daughter has not been involved."
A picture of the toilet block has been posted on Facebook page Wallasey Gossip and has garnered more than 200 comments.
Another mum said the open-plan toilet would only add to her daughter's anxiety issues.
She said: "She doesn't need to be looked at when heading to the toilet.
"Her and a few of her friends have now decided to not use that set of toilets, as there are other sets, at the moment, that are still enclosed for now.
"I feel that the girls are at risk of the boys looking in and over the top of the cubicle.
"My daughter has been told that the reason going round school for the change is to stop bullying, smoking and bunking in the toilets."
The school has not made any public comment.