Recent drone attacks in Pakistan and Afghanistan have again complicated relations with the U.S., a media report said.

“Two separate but similarly bitter disagreements over drone strikes in Pakistan and Afghanistan have complicated relations between the United States and those two countries at a delicate moment, again highlighting the political complications from America’s persistent reliance on the lethal remote-controlled weapons,” the New York Times said.

A recent drone strike in Afghanistan killed civilians forcing the U.S. military commander to apologise to President Hamid Karzai who was angry at the civilian deaths and had a renewed reason to refuse to sign a long-term security agreement with the United States.

In Pakistan’s tribal belt, a CIA drone strike yesterday killed a militant days after a major political party, as part of its campaign to end the drone strikes, publicly named a man it said was America’s top spy in the country.

“The use of these weapons, which is deeply resented, highlights the political costs to the United States of the drone campaigns, even as its range of military options in the region has started to narrow with American combat troops leaving Afghanistan,” the report added.

The U.S. military has restricted raids on Afghan homes, amid demands from Mr Karzai for a complete ban on such operations.

Afghan anger over one such raid last week led Mr Karzai to insist on a ban, and he has said he will not sign the long-term security agreement with the U.S. until such operations are definitively ceased.

“That leaves airstrikes, particularly by drones, as one of the last practical military options left to the American-led military coalition in Afghanistan,” the NYT report said.

The Pakistan Tehreek-i-Insaf party of former cricket star Imran Khan accused the director of the CIA and the man it identified as the agency’s Islamabad station chief, of murder.

Mr. Khan has said the strikes have jeopardised efforts to start peace talks with Taliban insurgents.