Ten of thousands of schools and university websites have become infected by hardcore pornographic content.
Schools have been targeted by "malicious spammers" who upload explicit sexual material linked to the schools' websites, according to Times Educational Supplement (TES).
Older versions of the free, open-source software Moodle, which allows teachers and pupils to create interactive websites was identified as the main problem.
It is understood that previous versions of Moodle software had been cracked by computer hackers, who were then creating user profiles on the sites to upload pornography, called "profile spam".
The software is used by 27 million people worldwide and even the most powerful school firewalls are unable to prevent users within schools accessing the pornographic material.
It was revealed last week that 20 primary schools, including St Dunstan's Primary in Birmingham, had been targeted.
Becta, the Government's educational technology agency, has launched an investigation.
Stephen Lucey, Becta's executive director of strategic technologies, said: "We have always placed the very highest priority on safeguarding learners while using the internet at school, and so we are concerned to hear of this case.
"We have a robust internet service provider accreditation scheme which ensures that suppliers from the scheme provide schools with in-built filters to block inappropriate or offensive material being accessed at school, and to date this have always proven to be very successful."
Moodle.com, the firm that produces the software, said efforts have been made to tell users to upgrade their software.
Martin Dougiamas, the founder, said flaws in the software had been "found and fixed".
"Profile spam is almost invariably not accessible from within the affected Moodle site itself" he said "The spammers usually can't join courses (and aren't interested in doing so) and so never come up as fellow participants for any actual pupils, and there is no link to these affected pages from within the school sites." (By Urmee Khan, Digital and Media Correspondent Last Updated: 12:34AM GMT 13 Feb 2009)