The former chief of the CIA on Tuesday praised Libyan leader Col. Gaddafi past cooperation and said his downfall could complicate US interests in the short term.

Retired general Michael Hayden, who led the Central Intelligence Agency from 2006 to 2009 under President George W. Bush, said that restive Syria also helped US intelligence but only in selective areas.

Speaking at a conference of the Marine Corps University, Hayden said the CIA had worked well with Col Gaddafi and Mussa Kussa, the foreign minister who defected last month as Libyan forces moved against rebels.

“Whatever you think of Col Gaddafi and Mussa Kussa... they were good and they were good counter-terrorism partners,” Mr Hayden told the conference near Washington.

Mr Hayden said Syrian President Bashar al-Assad was “pretty good” at fighting Sunni Muslim militants but supported Shiite radicals. Mr Assad belongs to the Alawite sect, a Shiite offshoot despised by Sunni extremists such as Al-Qaeda.

“In both cases, you have real near-term turbulence that could – that will – make the closer fight in the immediate time-frame much more difficult,” Mr Hayden said.

But he said the wave of unrest across the Arab world could prove beneficial to the US in the long term by changing the dynamics of the region.

The uprisings “will make the ground far less fertile for the type of extremism that Al-Qaeda proselytises, but it’s a long time between here and there,” Mr Hayden said.

Col Gaddafi, a long-time international pariah due to the 1988 Lockerbie bombing and other attacks blamed on Libyan spies, started to reconcile with the United States in 2003 and found common interests in fighting Al-Qaeda.

But Western powers led by France and Britain launched air strikes on Col Gaddafi’s forces last month due to fears of mass civilian casualties as they mobilised against rebel strongholds. Mr Hayden also voiced concern about Yemen, a frontline in the US-backed campaign against Al-Qaeda. President Ali Abdullah Saleh, a key US partner who has been in power for 30 years, has agreed to a plan to step down.

“I would never claim that President Saleh was, kind of, an easy fit as a partner with regard to anything. But I don’t know what’s on the next page,” Mr Hayden said.

“Now you’ve got the Yemeni government at best distracted and perhaps worse,” he said.