The Guardian has apologised after it implicated the Community Security Trust in a story attacking Education Secretary Michael Gove.

The newspaper ran a piece criticising Mr Gove's role in awarding government funding to the charity while he also sat on CST's advisory board. It quoted campaigner Professor David Miller, of Spinwatch, claiming Mr Gove should have stepped down from the grant process to avoid a conflict of interest.

The Education Secretary announced in December 2010 that the government would provide £2 million to fund security measures at Jewish schools.

Mr Gove has been on CST's advisory board for four years, but has never attended a meeting or offered any formal advice to the charity.

No one from the Guardian spoke to CST before the story was published online last Friday - Holocaust Memorial Day -and in the paper the next day.

A source close to Mr Gove said: "It is unbelievable to attack any politician for funding the protection of Jewish children. It is even more extraordinary, and frankly offensive, to do it on Holocaust Memorial Day." John Mann MP, chair of the All Party Parliamentary Group against Antisemitism, wrote to the Guardian on Wednesday attacking its "ill-conceived" report.

Mr Mann wrote: "The proposal that the state should fund the security costs of state schools was one of the 35 recommendations of the All-Party Parliamentary Inquiry into Antisemitism and was being enacted by Ed Balls when the election was called. It is appropriate and unsurprising that Michael Gove determined to meet the request."

The JC understands the Guardian had been preparing to publish its attack on Mr Gove for two weeks. A number of similar stories have already appeared in the paper this year.

A CST spokesman said the charity was "astonished that the Guardian has chosen to mark Holocaust Memorial Day by attacking the funding provided by the government to pay for security guarding at Jewish state schools. This funding is provided to protect Jewish schools against terrorism. This is a real threat.

"If the Guardian had contacted CST before running the story, we could have explained all this to them."

A Guardian spokeswoman denied the story was misleading, and said the CST had not been made aware of the story because it did not allege the CST "had done anything improper… We regret the timing of the piece's publication, which was entirely inadvertent… and regret any offence caused." The Guardian considered the issue of antisemitic attacks on schools to be "an important story and we will certainly cover it in future". The paper later amended its story to clarify that the CST does not retain any of the grant money.

Professor Miller's NeoCon Europe website has previously been forced to remove work by a writer who expressed antisemitic views.