US Defence Secretary Leon Panetta says the United States will continue to order drone air strikes on Pakistani territory whenever America has a need to defend itself.
On Tuesday, Pakistan summoned the US deputy ambassador to Islamabad to reiterate its serious concern about drone strikes.
The BBC reports there have been eight US drone strikes in the past two weeks despite demands for them to be stopped.
Pakistan says the drone attacks fuel anti-US sentiment and claim civilian casualties along with the targets. The US insists the strikes are effective.
al Qaeda's second-in-command, Abu Yahya al-Libi, was killed when two missiles were fired at compound early on Monday in Hesokhel, a village in the North Waziristan tribal area.
In Delhi on Wednesday, Mr Panetta made it clear that the US would continue to use unmanned drone aircraft in Pakistan.
We have made it very clear that we are going to continue to defend ourselves, he said. This is about our sovereignty as well.
He also said the drone strikes helped protect Pakistanis, who have been the targets of attacks by al-Qaeda and its allies.