THE CIA has been ordered out of a desert airbase in Pakistan from where it launched deadly Predator drone strikes against al-Qa’ida.

The Shamsi base in Baluchistan has been at the forefront of the US’s counterterrorism operations in the region. But the fall-out from the mission by US navy SEALs on May 2 to kill Osama bin Laden at his compound in Abbottabad appears to have finally brought to an end the secret arrangement with the CIA, which allowed the intelligence agency to hit terrorist and Taliban targets in North Waziristan on the border with Afghanistan.

Pakistani Defence Minister Ahmed Mukhtar said the US had been told to stop launching strikes from Shamsi. The move represents the latest blow to US-Pakistani relations, which have been seriously damaged since the killing of bin Laden.

Washington has made it clear that Pakistan must have colluded to hide the al-Qa’ida leader for five years within its borders. At the same time, Pakistan is furious the US engaged in a military strike on the Abbottabad compound without its knowledge.

Pakistani authorities have also claimed that dozens of women and children have been killed by the Predator attacks, and outrage over the strikes has sparked civilian protests.

The numbers are disputed by the US, where officials say no civilians have been killed since August last year and that about 30 died during the previous 12 months.

Mr Mukhtar said: “We have told them to leave the airbase.”

The news took the US by surprise yesterday. The CIA declined to comment, but a US official said: “This is news to us. American operations against terrorists in Pakistan are continuing.”

Since President Barack Obama took office in 2009, the number of Predator attacks from Shamsi has accelerated, resulting in the deaths of 20 of the 30 most wanted al-Qa’ida leaders hiding in Pakistan’s tribal northwest.

The most recent success was last month, when Ilyas Kashmiri, an al-Qa’ida leader with a $US5 million bounty on his head, was killed by a CIA Predator strike. Kashmiri is believed to have played a key role in planning the 2008 terrorist attacks in Mumbai. He was also one of four or five names on a list handed to the Pakistan government last month by US Secretary of State Hillary Clinton as the extremists the US wanted hunted down in joint operations with Pakistani.

Anticipating the closure of Shamsi, the CIA has been shifting some operations from Pakistan to Afghanistan and is understood to have a base at Jalalabad, in eastern Afghanistan, from where it has been launching strikes.

However, the increasing political and military tensions between Pakistan and the US could increase should the drone strikes continue, even if they are launched from Afghanistan, because such a move would breach Pakistani sovereignty.

The closure of the operations at Shamsi, a small airfield about 320km southwest of Quetta, would be a blow for the CIA, although with relations between Washington and Islamabad at such a low ebb it seemed unlikely the base would remain a permanent location for secret missions. Pakistani politics and growing anti-US sentiment in the country made it inevitable the CIA would have to find alternative arrangements for its Predators.

General David Petraeus, who is due to take over as director of the CIA on September 1, will be landed with the Pakistan issue on his first day at the agency’s headquarters in Langley, Virginia.