Overall, the quality of school buildings in Wales has improved little in the past five years, says its annual report, published this week.
The Welsh Assembly government has pledged that all schools will be "fit for purpose" by 2010, and promised pound;560 million for improvements by 2007.
But Estyn's report shows much more cash is needed, according to Brian Lightman, of the Secondary Heads' Association Cymru.
In 2003-4 more inspectors than ever before commented on the state of school toilets, according to Estyn's report. Although most are in good condition, there are too few in some schools.
Many lack the basics for good hygiene - soap, towels or hand dryers - so could be endangering pupils' health. Meanwhile, at a few schools, pupils or staff are still having to traipse outdoors to answer the call of nature.
Primary school buildings overall have improved a little over the past five years, with three-fifths now considered good or very good. But there has been no improvement in the facilities enjoyed by secondary pupils and teachers, with only a quarter rated good or very good and around a fifth considered sub-standard.
Inspectors identified problems in half of last year's reports on secondary schools. "Many of these key issues are about the poor state of the school library or sports facilities. Schools do not have the money to pay for the new buildings or the major improvements and repairs that they need," says the report.
An Assembly government spokesperson said: "The Assembly has put substantial investment into improving school buildings and we expect local authorities to put this to good use."
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