At least one local militant was wounded in the attack in the South Waziristan tribal region near the Afghan border, said the two officials, speaking on condition of anonymity because they were not authorized to talk to the media.
The U.S. has launched dozens of similar attacks in recent years in Pakistan's tribal areas, where al Qaeda and Taliban fighters have sought sanctuary to stage attacks across the border into Afghanistan. The strikes have provoked protests from Pakistani officials and residents in the tribal areas saying they are a violation of the country's sovereignty.
The three militants killed were from a Central Asian country, said the officials without providing further details. They said they received information about the attack from local agents.
Pakistani military officials were not immediately available for comment. Washington usually does not confirm such strikes.
The U.S. has also pushed Pakistan to crack down on militants in the tribal areas. The Pakistani military launched an operation Tuesday in the Khyber tribal region to secure the major supply route to U.S. and NATO troops in Afghanistan, which has been repeatedly attacked by militants.
The top Khyber administration official, Tariq Hayat Khan, said Thursday that the operation was 80 percent complete, having destroyed 33 militant hideouts with artillery and helicopter gunships and arrested 43 Pakistanis. Pakistan closed the route through the famed Khyber Pass when it started the operation, but Khan predicted it would reopen "in a day or so."
Western forces in landlocked Afghanistan rely on the winding, mountainous road for delivery of up to 75 percent of their fuel, food and other goods, which arrive in Pakistan via the port city of Karachi. The U.S. military has praised the Pakistani campaign and said the temporary closure of the road was not a problem.
Meanwhile, militants fired four rockets at a government building in the town of Khar in the Bajur tribal region Thursday, killing at least four people and wounding 16 others, said local government official Israr Khan. The wounded were transported to a hospital for treatment, he added.
The Pakistani military has conducted an intermittent campaign against insurgents in Bajur, an area that has also been targeted by several U.S. missile strikes.
The Pakistani government also has faced a low-level insurgency in the southwest province of Baluchistan, where militant tribesman accuse the government of pocketing too much revenue from the region's natural gas reserves and ignoring development needs.
Suspected tribesman attacked a gas purification plant in the Baluchistan town of Uch with rockets and gunfire on Thursday, killing three soldiers and wounding five others who were defending the facility, said Maj. Gen. Salim Nawaz.
He said the soldiers killed 10 of the attackers during the assault, some 300 miles east of the provincial capital of Quetta.
Also Thursday, a bomb destroyed a small police outpost on the outskirts of the northwest city of Peshawar, killing one policeman, said local police official Noor Illahi Khan.
By Associated Press Writer Ishtiaq Mahsud; AP writers Habib Khan, Riaz Khan and Abdul Satter contributed to this report from Khar, Peshawar and Quetta