Defence Secretary Leon Panetta said Tuesday the United States is waging “war” in Pakistan against militants, referring to a covert campaign the CIA steadfastly refuses to publicly confirm.

It was Panetta’s latest comment acknowledging drone bombing raids in Pakistan, an open secret that the US government declines to discuss publicly.

Speaking to an audience at the Woodrow Wilson Center in Washington, the former CIA director pointed to a “complicated relationship” between Washington and Islamabad.

“And admittedly, there are a lot of reasons for that. We are fighting a war in their country,” Panetta said.

“They have in fact given us cooperation in the operations of trying to confront Al-Qaeda in (tribal areas)… And they continue to work with us.”

But he said the two countries had sharp disagreements over “the relations they maintain with some of the militant groups in that country”, a reference to Washington’s demand that Islamabad crack down on the Haqqani network.

During a visit to US bases in Italy last week, Panetta made two casual references to the CIA’s use of armed drones.

“Having moved from the CIA to the Pentagon, obviously I have a hell of a lot more weapons available to me in this job than I did at CIA — although Predators aren’t bad,” Panetta told an audience of sailors at the US Navy’s Sixth Fleet headquarters in Naples.

Bombing raids by robotic unmanned US aircraft dramatically increased under President Barack Obama, with the CIA operation focusing on Al-Qaeda and Taliban figures in northwest Pakistan.

About 30 drone strikes have been reported in Pakistan since elite US Special Operations Forces killed Al-Qaeda chief Osama bin Laden in May near the country’s main military academy in Abbottabad, close to the capital.

US officials did not notify Pakistan in advance of the raid, and Panetta — the CIA chief at the time — subsequently said the US government feared that bin Laden would be tipped off about the operation beforehand.

An American drone is also believed to have killed US-born Al-Qaeda cleric Anwar al-Awlaqi in Yemen last month.