A former White House security expert has said the Bush government did not consider terrorism to be an urgent threat before 11 September 2001.
The White House has rejected Mr Clarke's allegations
Richard Clarke told a commission that before the attacks the government considered terrorism "an important issue, but not an urgent issue".
He apologised to the families of the 3,000 victims for the "failures" that allowed the attacks to take place.
Earlier, CIA director George Tenet said a specific warning had been impossible.
Mr Clarke began his attack on Monday when he accused President George W Bush's administration of ignoring the threat from terror attacks because of a fixation on Iraq.
In a book published this week, Mr Clarke accused Mr Bush of ignoring warnings before the attacks.
In his testimony on Wednesday, Mr Clarke, who quit his post last year, said Mr Bush was told "dozens of times" that there was an urgent terror threat during 2001.
George Tenet, CIA director
Samuel Berger, former national security adviser
Richard Clarke, former counter-terrorism co-ordinator
Richard Armitage, Deputy Secretary of State
"There was a process under way to address al-Qaeda, but although I continued to say it was an urgent problem, I don't think it was ever treated that way," he told the commission investigating how the attacks were able to take place.
Although he admitted that an attack could not have been prevented even if his recommendations had been adopted, he made it clear he believed the White House should have done more.
Mr Clarke also reiterated his criticism of the decision to invade Iraq, saying Mr Bush had "greatly undermined the war on terrorism".
Mr Clarke began his testimony by offering an apology to victims of the attacks.
"Your government failed you, those entrusted with protecting you failed you and I failed you... For that failure, I would ask... for your understanding and forgiveness," he said.
It is believed to be the first such apology by a public figure.
Meanwhile, the White House sought to discredit Mr Clarke, releasing a previously anonymous press briefing which show him praising the president's anti-terrorism strategies.
"He needs to get his story straight," said Condoleezza Rice, National Security Adviser and Mr Clarke's former boss.
Mr Clarke served as head of counter-terrorism under four consecutive US presidents, from Ronald Reagan to George W Bush.
Earlier, CIA director George Tenet said warnings had "lit up" in the weeks before 11 September - but had been thin on specifics.
"They indicated that multiple spectacular attacks were planned and that some of the plots were in their final stages.
Investigating US policy before, and response after 9/11 attacks
Bipartisan: Five Democrats, five Republicans
Set up by Congress, Nov 2002
Eight public hearings so far, three more to go
President Bush to meet privately with panel leaders
To report findings on 26 July
"The reporting was maddeningly short on actionable details. The most ominous reporting... was also the most vague."
Later, the US Deputy Secretary of State Richard Armitage defended his government's record.
He implied the previous administration had been partly at fault.
"When we came into the administration, I found a State Department that had been neglected for 12 years - in terms of management, budget, and almost everything else," he told the panel.
This is the eighth public hearing held by the bipartisan commission, established in 2002.
In a preliminary report on its findings so far, the commission has said that the Clinton and Bush administrations were too slow in moving away from diplomatic pressure to direct military action as a way of dealing with the al-Qaeda leadership.