The morning-after pill is among services offered to pupils
Sexual health clinics are available in nearly 30% of secondary schools in England, according to a survey.
Research by the Sex Education Forum suggested one in six on-site clinics offered the morning-after pill, and all provided condoms or pregnancy tests.
The results had angered some parents' campaigners who said they were being left "out of the loop" by schools.
But the forum said the majority of schools would have talked to parents or governors before setting up clinics.
Lucy Emmerson, a senior development officer at the forum, said: "Parents with children in those schools will know that the support services will involve sexual health advice and what the range of services on offer are.
"Also, health professionals always encourage the young person to talk to their parents about any problems they are experiencing," she said.
But Ms Emmerson added it would be illegal for a school to breach a patient's right to anonymity.
Her report will be published on Tuesday.
The forum, a group which supports the development of sex and relationship education in schools, sent questionnaires to local authorities across England, of which 70% responded.
The survey also found one in six schools with clinics provided tests for diseases like chlamydia.
A report in the Observer newspaper suggested one in 20 school-based clinics were providing prescriptions for contraception without parents being informed.
Co-founder of the Parent Organisation support group Andy Hibberd said: "It is not a problem that children are getting sex advice in school but the fact that parents are being intentionally cut out of the loop is wrong.
"If they want the morning-after pill, the school will sanction that and the parent will never know.
"We would say that this is the end of innocence."
But forum member Brook, a young people's sexual health advice charity, said the survey results were "brilliant news".
Brook chief executive Simon Blake said: "All the evidence shows that if good quality sex education starts early enough, it can be part of the solution to problems of teenage pregnancy and sexually transmitted disease."
The survey comes after official figures for England and Wales found the number of abortions among girls aged under 16 rose by 10% to 4,376 in 2007.
In the under 14s, abortions rose by 21% from 135 in 2006 to 163 last year. The number of abortions in all women rose by 2.5% to reach an all time high of almost 200,000.
In response, government advisers called for high quality sex education at school and investment in contraception services for young people.