The Times said the CIA struck a secret deal with Pakistani counterparts to gain access to airspace over the tribal regions of western Pakistan where many al-Qaida operatives had fled to escape bombings in neighboring Afghanistan. In return, the CIA agreed to target enemies of Pakistan's Islamabad-based national government, which for years has fought to bring the tribal militias under their control.
"We have repeatedly affirmed that Pakistan regards the use of drone strikes as counter-productive," Foreign Office spokesman Aizaz Ahmed Chaudhry told the Associated Press of Pakistan, the government's official news agency.
The Times account highlighted the assassination of Nek Muhammad, a Pakistani tribal warlord who had successfully managed to fend off government forces and forced the central government into peace negotiations.
The militia Muhammad had assembled included many al-Qaida and Taliban members who had crossed the border into Pakistan -- and who regarded Islamabad's support of the American efforts in Afghanistan as treasonous.
Muhammad was killed in a drone strike carried out by the CIA for the Pakistanis in 2004, the Times said.
Both governments have officially refused to recognize the attack.