The CIA chief said that globally, al-Qaeda had suffered "significant setbacks - as a lot of the Islamic world pushes back on their form of Islam".
The upbeat assessment came after a US intelligence report last August said al-Qaeda had regrouped in Pakistan's border region with Afghanistan and was planning new attacks on the US.
Despite the assessment, some analysts warned against presumptions that the network had been defeated.
"It could well be the administration is trying to get Americans to believe we've won against al-Qaeda so they don't get accused of going after Iran before al-Qaeda is defeated"
Michael Scheuer, former head of CIA bin Laden unit
Michael Scheuer, former head of the CIA's bin Laden unit, told Al Jazeera that the US had made too much out of perceptions that there was dissent against al-Qaeda in the Middle East and that bin Laden's objectives had been in many respects achieved.
"[Al-Qaeda] certainly have problems, they're fighting wars in two different places against the world's most powerful military, but they're not doing that badly," he said.
"If you look at it from al-Qaeda's perspective, bin Laden has encapsulated their effort in three terms - bleed American into bankruptcy, spread out the American military and intelligence forces so they're not flexible or responsive and try to disrupt political harmony within the US."
"If I'm bin Laden I'm pretty happy about the way the war looks to me at the moment."
Scheuer said that the real reason for Hayden's comments may be the US's ongoing strategic relationship with Israel and a desire within the US administration to put the option of action against Iran back on the agenda.
"It could well be that the administration is trying to get Americans to believe we've won against al-Qaeda so they don't get accused of going after Iran before al-Qaeda is defeated," he said.
"On Wednesday, having al-Qaeda to be number one enemy of the US and on Thursday to have the CIA director and the director of homeland security say 'no, that's yesterday's news' I have to think that some kind of confrontation with Iran is back on the front burner."
But Hayden said gains had been made against al-Qaeda and that US intelligence agencies had carried out several attacks since January, using unmanned aircraft to strike safe houses.
|Hayden said capturing or killing Bin Laden or|
al-Zawahiri, right, was still a priority [EPA]
"The ability to kill and capture key members of al-Qaeda continues, and keeps them off balance - even in their best safe haven along the Afghanistan-Pakistan border," Hayden told the newspaper.
He also said al-Qaeda's global leadership had lost three senior officers since the start of the year.
Two of those had succumbed "to violence", an apparent reference to missile strikes from US drone Predator aircraft in Pakistan, the Post reported.
Hayden said capturing or killing bin Laden and his top deputy, Ayman al-Zawahiri, remained a top priority although he said it would be difficult to find them in a region where the US military is officially forbidden to operate.
In Iraq, he said he was encouraged by US success against al-Qaeda's allies and by what he said was the steadily rising competence of the Iraqi military and growing popular opposition towards radical armed groups.
"Despite this 'cause celebre' phenomenon, fundamentally no one really liked al-Qaeda's vision of the future"
Michael Hayden, head of the CIA
"Despite this 'cause celebre' phenomenon, fundamentally no one really liked al-Qaeda's vision of the future," Hayden said.
He added that violence against US and Iraqi government forces was viewed by Iraqis as "more and more a war of al-Qaeda against Iraqis".
Hayden said leading Sunni preachers - including some who used to support al-Qaeda - had condemned the group for its killing of Muslim civilians.
However, the Post said Hayden expressed concern that the progress against al-Qaeda could be halted or reversed because of what he views as growing complacency and a return to the mind-set that existed before the September 11 attacks.