Embarrassingly, the British Educational Communications and Technology Agency (Becta), which gets more than pound;30 million annually to tell schools how to use computers, was forced to shut down its website for three days after the attack.
Hackers calling themselves "the r00ted team" took control of the website on Saturday, leaving an email address and a note which said "r00ted Team ownz ur (operating system)".
Agency staff said the site was not altered or defaced but admitted the incident was highly embarrassing.
Last year Becta published a leaflet saying: "Even organisations without specific secrets or secure information to hide can find themselves the target of attacks, which can result in loss of data or services. There are many hacking tools available on the Internet that require little skill or knowledge to use."
A Becta spokesman said there was no evidence that the agency had been targeted because of its work with schools. "The hackers don't seem to have had a political motive," he said. "It's simply that we are a government agency with a website.
"There are some slightly embarrassed faces. It is a good reminder that security is a key issue and every effort will be made so this does not happen again."
Russell Ingleby, chair of the Association for Information and Communications Technology in Education and ICT co-ordinator at Westmoor junior school in Kirklees, said teachers would continue to value Becta's advice. "Any website can be attacked by hackers," he said. "Becta have been doing an excellent job and their support for schools has been first rate."
Mr Ingleby said that teachers in ACITT had noticed a sharp rise in the amount of unwanted "spam" emails and viruses which had been sent to their schools over the past 12 months.