NEW YORK: American intelligence agencies are concerned that they could lose drone bases in Pakistan and Afghanistan if Afghan President Hamid Karzai does not sign a controversial security deal with the United States, the New York Times reported on Monday.

The new concerns reflect how US troop levels in Afghanistan directly affect long-term American security interests in neighbouring Pakistan, the Times said, citing administration, military and intelligence officials.

The Obama administration has already organised a team of intelligence, military and policy specialists to devise alternatives to reduce the damage if their attempt to reach the deal fails.

American officials say the agreement was completed last year and has urged Karzai to enact it as soon as possible. But the Afghan president set out conditions for Washington, including the US military must first end its deadly drone strikes and night raids on Afghan homes, which have left hundreds of civilians dead.

US President Barack Obama has threatened to withdraw all American troops from Afghanistan if the deal is not struck. In that case, the CIA's drone bases in the country would have to be closed, according to administration officials, because it could no longer be protected, the Times said.

American intelligence agencies say the nearest alternative bases are too far away for drones to reach the mountainous territory in Pakistan, where the CIA claims is a hideout for militants.

The Pakistani government also is unhappy with the US drone operations saying the strikes kill local civilians.

According to the Times, the American agencies are also concerned that the nearest alternative bases would be too distant to monitor and respond as quickly as American forces can today if there were a crisis in the region, such as missing nuclear material or weapons in Pakistan and India.