Richard Clarke said on Tuesday that the conflicting assessments of risk showed how some officials sought to inflate the threat for political gain.
He specifically focused on differences in opinion between US Homeland Security Secretary Tom Ridge and US Attorney General John Ashcroft.
Clarke is not alone in highlighting inconsistencies over security warnings from different members of the administration.
The Washington Post also reported that Ridge allies within the Bush administration and members of Congress criticised Ashcroft for failing to co-ordinate threat information with the White House and Homeland Security.
Last week, the attorney general said: "We're going into the summer and we should have heightened security but we have no new intelligence about it".
Clarke derided the comment as "ass-covering, or perhaps, dare I say it, politics in an election year."
The former adviser is currently in Berlin on a book tour to promote his unflattering account of US President George Bush's policies, entitled Against All Enemies.
The book is riding the wave of
criticism of the US war on terror
Clarke has been an outspoken critic of Bush's security policies ahead of and after the attacks of 11 September 2001.
He has accused Bush of failing to pay enough attention to the al-Qaida threat after he took office in January 2001 and undermining the struggle against terrorism with a "counterproductive" war in Iraq.