The Community Security Trust and Department for Education have defended Education Secretary Michael Gove following criticism of his role in awarding government funding to the Jewish organisation while also acting on its advisory board.
The Spinwatch organisation, which "monitors spin in contemporary society", said Mr Gove should have stepped down from the grant process due to his position on the board.
The Guardian reported Spinwatch campaigner David Miller's claim that Mr Gove's role represented a conflict of interest.
CST said it was "astonished" by the "misleading" criticism. Mr Gove has been on the advisory board for four years.
In December 2010 he announced the government would provide £2 million to fund security measures at Jewish schools.
Spinwatch said it was "blindingly obvious" that the Education Secretary should have stepped down from his role in awarding those grants.
The Department for Education said: "Officials were aware that the Secretary of State was listed as a member of the CST advisory board. The then Permanent Secretary was fully content that there was no conflict of interest.
"The advisory board has around 55 to 60 members, drawn from a cross-section of society including Members of Parliament and peers, police, the armed forces, academia and religious and lay leaders of the Jewish community.
"It is not part of the governance structure of CST and its members have no responsibility for, and play no part in, the day-to-day management of the charity. The advisory board itself does not meet as a separate body."
A CST spokesman said: "We are 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.
"The money is merely administered by CST and distributed in full to Jewish schools who then use it to employ their own security guards. We are proud of our role in helping this to take place.
"If the Guardian had contacted CST for comment before running the story, we could have explained this to them."
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."