Britain's former spy chief accused the BBC of "parroting" Al Qaeda propaganda to children as young as six.
Dame Pauline Neville Jones, who is also a former BBC governor, is infuriated at the stance the corporation's Newsround programme took on the September 11 attacks.
She accused the flagship children's news bulletin of feeding an "ugly undercurrent" which suggests the terrorist outrage was somehow justifiable.
Newsround is aimed at viewers aged between six and 12.
On its website it answered the question concerning 9/11, "Why did they do it" by saying: "The way America has got involved in conflicts in regions like the Middle East has made some people very angry, including a group called al Qaeda - who are widely thought to have been behind the attacks."
After the public complained, the text was amended.
It now reads: "Al Qaeda is unhappy with America and other countries getting involved in places like the Middle East.
"People linked to al Qaeda have used violence to make this point in the U.S.A, and in other countries."
Dame Pauline, who headed the Government's Joint Intelligence Committee and is described as the most formidable female diplomat Britain has produced, said the new version was even worse.
"It still says it's all America's fault, and now for daring to be involved in the Middle East at all," she said.
"It wasn't 'people linked to' al Qaeda who killed 3,000 people that day, it was al Qaeda itself.
"Osama bin Laden even boasted of the attacks. Is the BBC really saying that if you're 'unhappy' it's quite normal behaviour to murder people?
"Is the BBC so naive as to take al Qaeda's propaganda at face value? Or is there something more sinister at work here?"
Dame Pauline, who is now a shadow security spokesman, added: "Al Qaeda make the manifestly false claim that America is part of an enormous Jewish-Christian conspiracy to dominate the world and kill Muslims.
"This is no secret - Osama bin Laden has said as much himself.
"We know that in the long run the struggle against terrorists is a battle for hearts and minds.
"How can we expect to win when our national broadcaster is parroting their line to our own children?
"There is only one set of people who are ever to blame for terrorist attacks and that's the perpetrators themselves."
Dame Pauline said the BBC was a "national treasure" and she had been proud to serve as a governor.
"But from time to time I have found myself asking questions about BBC's attitude to terrorism. It even orders its journalists not to use the word terrorist," she added.
"Although almost everyone in Britain quite rightly reacted with horror to the attacks of September 11, there was an ugly undercurrent that blamed America for being attacked.
"Just two days after the attacks the BBC screened an edition of the Question Time programme where they invited an anti-American audience that laid into the American ambassador, leaving him close to tears. In fairness, the BBC apologised for that outrage.
"Even though this was an appalling example of knee-jerk prejudice, at least it was meant for adults.
"I never imagined the rot would spread to the BBC's children's programmes. I was wrong."
Dame Pauline has complained to the BBC's head of journalism Mark Byford, who is understood to have defended the text as "clear and concise".
Sinead Rocks, editor of the Newsround programme, said the first version of the text was several years old and should no longer have been available.
But she defended the new version, insisting it was not an attempt to "justify" the events of September 11.
"We feel it is entirely legitimate to question the motives of the people who carried out the attacks," she said.
"Our contact with our audience has shown that their understanding is helped by events being put into some kind of context.
"We often have to translate complex and emotive issues into language appropriate for children. It's a responsibility we take very seriously."
