But in a book written from inside an Egyptian prison, he has launched a frontal attack on al-Qaeda's ideology and the personal failings of bin Laden and particularly his Egyptian deputy, Ayman al-Zawahiri.
Twenty years ago, Dr Fadl became al-Qaeda's intellectual figurehead with a crucial book setting out the rationale for global jihad against the West.
Today, however, he believes the murder of innocent people is both contrary to Islam and a strategic error. "Every drop of blood that was shed or is being shed in Afghanistan and Iraq is the responsibility of bin Laden and Zawahiri and their followers," writes Dr Fadl.
The terrorist attacks on September 11 were both immoral and counterproductive, he writes.
He is equally unsparing about Muslims who move to the West and then take up terrorism.
In particular, Dr Fadl focuses his attack on Zawahiri, a key figure in al-Qaeda's core leadership and a fellow Egyptian whom he has known for 40 years. Zawahiri is a "liar" who was paid by Sudan's intelligence service to organise terrorist attacks in Egypt in the 1990s, he writes.
The criticisms have emerged from Dr Fadl's cell in Tora prison in southern Cairo, where a sand-coloured perimeter wall is lined with watchtowers, each holding a sentry wielding a Kalashnikov assault rifle. Torture inside Egyptian jails is "widespread and systematic", according to Amnesty International.
Zawahiri has alleged that his former comrade was tortured into recanting. But the al-Qaeda leader still felt the need to compose a detailed, 200-page rebuttal of his antagonist.
The fact that Zawahiri went to this trouble could prove the credibility of Dr Fadl and the fact that his criticisms have stung their target. The central question is whether this attack on al-Qaeda's ideology will sway a wider audience in the Muslim world.
Fouad Allam, who spent 26 years in the State Security Directorate, Egypt's equivalent of MI5, said that Dr Fadl's assault on al-Qaeda's core leaders had been "very effective, both in prison and outside".
He added: "Within these secret organisations, leadership is very important. So when someone attacks the leadership from inside, especially personal attacks and character assassinations, this is very bad for them."
A western diplomat in Cairo agreed with this assessment, saying: "It has upset Zawahiri personally. You don't write 200 pages about something that doesn't bother you, especially if you're under some pressure, which I imagine Zawahiri is at the moment."
Dr Fadl was a central figure from the very outset of bin Laden's campaign. He was part of the tight circle which founded al-Qaeda in 1988 in the closing stages of the war against the Soviet occupation of Afghanistan. By then, Dr Fadl was already the leader of Egyptian Islamic Jihad, an extremist movement which fought the Cairo regime until its defeat in the 1990s.
Dr Fadl fled to Yemen, where he was arrested after September 11 and transferred to Egypt, where he is serving a life sentence. "He has the credibility of someone who has really gone through the whole system," said the diplomat. "Nobody's questioning the fact that he was the mentor of Zawahiri and the ideologue of Egyptian Islamic Jihad."
Terrorist movements across the world have a history of alienating their popular support by waging campaigns of indiscriminate murder. This process of disintegration often begins with a senior leader publicly denouncing his old colleagues. Dr Fadl's missives may show that al-Qaeda has entered this vital stage.