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Umer Farooq, believed to be in charge of Al Qaeda's operations in Pakistan and Afghanistan, in a US drone attack in in the Khar Tangi area of Datta Khel district of Pakistan's troubled North Waziristan region, a day after the chief of the terror group's global operations was also killed in a Pakistani military operation.
A security official said Farooq was among five people killed when two missiles fired from the drone hit a compound.
The compound was completely destroyed in the attack.
His killing came a day after Pakistani forces killed top al-Qaeda operative Adnan Shukrijuma in raid at a house in South Waziristan.
The chief of Al Qaeda's global operations, Shukrijuma was wanted by the US over a 2009 plot to attack the New York subway system.
Shukrijuma was among the five men indicted in the US over the plot to bomb New York's subway system under orders from Al Qaeda leaders in Pakistan.
The New York indictment links him to the Manhattan plot and a similar never-executed scheme to attack British subways, according to media reports.
North Waziristan has long been used as shelter by the Taliban and Al Qaeda-linked militants and has frequently been targeted by US drones.
The Pakistani military launched a major offensive in North Waziristan in June and say they have killed more than 1,000 militants so far.
For almost a decade, American drone strikes in Pakistan's tribal belt have been deeply unpopular with the public.
Pakistani officials have publicly condemned the drone strikes, saying they violate sovereignty.