Scotland's Commissioner for Children and Young People has launched a campaign for new guidelines to improve school toilets.
Tam Baillie said the quality of the facilities must be monitored and guaranteed in the same way as workplaces for adults.
He argued the move was needed to ensure "dignified and safe facilities".
Local councils said improvements might cost lots of money that councils "do not have".
The Commissioner's views are set out in a report called Flushed with Success: Setting the Standard for Scotland's School Toilets.
Chief Medical Officer for Scotland, Sir Harry Burns, said: "I would like to see the guidance for school toilets updated, to ensure that basic hygiene standards including access to hot water and soap and proper hand washing facilities, are adhered to in every single school in Scotland."
The report follows a survey of 2,000 young people carried out by Ipsos MORI.
It found that nearly half of kids said they try to avoid school toilets, only using them if they "really had to", and another 10% said they never used them.
Asked about the availability of soap for handwashing, over a third of those who took part (37%) said their loos were "poor" or "very poor".
And for overall cleanliness, again about a third (33%) rated theirs "poor" or "very poor".
What are your school toilets like?
We asked you about this one: whether you like your loos, or find them disgusting?
Here are a few of the comments you sent in.
My school toilets in secondary school are great. But in primary school they were disgusting, the locks kept breaking and when we asked to get new ones we got shouted at. They said they cleaned them but I think they didn't.
I go to an all-girl secondary school and the toilets there are very dirty. People have drawn graffiti all over the walls. I think it could do with quite a few improvements!
My school loos are very poor, when its raining there's leaks and never really any soap I try very hard to avoid them.
Ammy, London, England
Our toilets are OK. The door sticks a bit and we think that we need more toilets as we have to wait sometimes.
Maggie, llkeston, Derbyshire
I'm in high school and I can tell you even though they are better than primary school toilets the girls use it as a way to use mobile phones.
Grace, Warrington, England
Our toilets are nice and clean. They are colourful with lots of soap and hot water. There is always toilet paper and our cleaners and caretaker make sure that they are always clean and safe to use. Our school council made a video to show people how to wash their hands properly.
From a junior school in Neath, Wales
Some of our toilet lids and things are broken, so I think some of those could be renewed.
I don't think they're the cleanest toilets I've ever been in, but they're also not the dirtiest. I think they could do with improving.
There are three cubicles in the boys' toilets and one of them is broken so it definitely needs renewing.
Quite a lot of the locks on the toilet doors are quite stiff. Also the toilets in Year 1, the hand dryer doesn't blow enough air out. It would take ages to dry your hands properly underneath it!
Some of the soap dispensers are jammed which is frustrating. Also there is only one toilet block for the year group, so at play-times they get extremely busy.
People don't flush the toilets. It's disgusting!
From a class at a school in Hailsham, England
My school toilets are dirty and smelly after only ten minutes of being at school. :(
Sharday, London, England
My school toilets are fairly new but they smell and the floors and ceilings are always smothered in toilet roll.
Millie, south east London, England
The toilets at my school are pretty clean thanks to our janitors but sadly a lot of times waste is left over from the younger kids.
My school loos are fine.
Jessica, London, England