Learning and Teaching Scotland has now embarked on a survey to assess the position on internet access in schools and to investigate whether a national strategy is possible.
Nick Morgan of the National Grid for Learning said: "Content filters are a crude form of software. They are valuable tools, but it is an unfortunate consequence that they can block the most innocuous materials. These include sites on military history because they contain violence, or on the suffragettes because they mention sexual liberation."
Websites run by the youth information organisation Young Scot, the sexual health service Young Caledonia and the Executive's own agency NHS Health Scotland are among those affected.
The problem stems from "firewall" content filters installed on all school and public library computers. These are aimed at protecting young people from pornographic, violent or racist content or from accessing chat rooms where they may be contacted by paedophiles.
They operate mainly by blocking "banned" words and phrases such as sex and sexual health, which also feature on sites aimed at positive health promotion. A study published last year in the Journal of the American Medical Association found that a quarter of health-related websites are blocked by internet filters, as are up to one in two sites on sexual health.
"There is no unsuitable content on our site yet young people are failing to get through," Louise Macdonald, Young Scot communications manager, said.
Young Scot is now embarking on a campaign to alert authorities and schools to the problem and to ask for the software to be overridden.
"I can understand local authorities are concerned and nervous about inappropriate materials, but there is a wider issue here about supporting and educating young people and helping them make informed choices for themselves," Ms Macdonald said.
Scotland remains among the worst hit countries in Europe for teenage pregnancies, while the incidence of the sexually transmitted disease chlamydia -common among under-25s - is rising, particularly in the Greater Glasgow and Lothian health board areas, according to the latest figures from Health Protection Scotland.
Meanwhile, pupils wishing to find out about contraception on the Young Caledonia website will be disappointed. The organisation, which has just received a pound;1.5 million extension of its funding from the Executive, is considering following Young Scot's lead and urging local authorities to lift the block.
One group that successfully made a case for its website to be unblocked by Edinburgh City Council is LGBT (Lesbian, Gay, Bisexual and Transgender) Youth Scotland. Fergus MacMillan, its policy manager, commented: "Our client group is an invisible population. It should be able to access information and advice in schools without having to ask a teacher."
But Tony Waclawski, health education improvement service officer for Glasgow, said: "It is difficult to unblock these websites without letting undesirable materials in. Schools have limits to their understanding of this process. Our main focus is delivering the curriculum, not free access to the internet in schools."
Susan Dean of the Scottish Drugs Forum said: "Schools should be educating children about drugs and drug use so they are then able to assess for themselves whether the information they come across on the web is worthwhile, rather than simply restricting their access to this material."
Judith Gillespie of the Scottish Parent Teacher Council accused authorities of cocooning pupils. "They should be allowing greater access to internet materials at the same time as equipping children to deal with its dangers."
The SPTC has recently produced a training pack on internet safety but so far fewer than 200 schools have requested it. "Schools lack training and knowledge in this area," Mrs Gillespie said.