"There is every reason to believe that these two top terrorist figures are dead," the official said, adding that the Kenyan-born pair was killed "within the last week".
"These deaths are a significant near-term degradation of al-Qaeda's leadership."
Pakistani security officials had reported that an unmanned US drone fired missiles in the Karikot area in South Waziristan on January 1 killing several foreign fighters.
"They died preparing new acts of terror," a CIA official said, speaking on condition of anonymity.
Al-Kini was involved in the truck bombing of the Marriott hotel in Islamabad that killed 55 people last September, according to the counterterrorism official.
The al-Qaeda leader was also allegedly behind an unsuccessful attempt to kill Benazir Bhutto, the former Pakistani prime minister, who was later assassinated in a separate attack.
|Rauf was reportedly killed in a US drone
attack last November [AFP]
The two men were also on the FBI's list of most wanted terrorism suspects and had been indicted for the 1998 bombings of US embassies in Tanzania and Kenya, and believed to have trained operatives to travel to the US and Europe.
The CIA has been known to conduct drone strikes in Pakistan's autonomous northwest tribal region, prompting Pakistan to condemn the attacks as a violation of sovereignty.
A US drone attack in November killed Rashid Rauf, the alleged al-Qaeda mastermind of a 2006 transatlantic aircraft bombing plot.
US forces in Afghanistan have carried out about 30 missile strikes in Pakistan in 2008, according to a Reuters tally, mostly since the beginning of September.
Osama bin Laden, al-Qaeda's top leader, and his deputy, Ayman al-Zawahiri, are believed to be hiding in the Afghan-Pakistan border area.