Swedan is said to have been Kini's top aide
Al-Qaeda's operations chief in Pakistan and another top aide have been killed, US and Pakistani sources say.
Kenyans Usama al-Kini and Sheikh Ahmed Salim Swedan were killed last week by a missile fired from a US drone near the Afghan border, the sources said.
Kini was believed to be behind last year's deadly attack on the Marriott hotel in Islamabad, US officials said.
Fifty-five people were killed when a truck packed with explosives rammed the hotel in September 2008.
A Pakistan government official, requesting anonymity, told the BBC the two men were killed along with a militant from Pakistan's Punjab province in South Waziristan, on Pakistan's border with Afghanistan.
A US counter-terrorism official said it was strongly believed that they were killed in a missile strike by a CIA drone aircraft on a building on 1 January.
The Pakistani military said it was conducting its own investigation.
Kini was involved in the Islamabad Marriott attack, officials say
The men - both born in Kenya - were on the FBI's most-wanted list over the 1998 bombings of US embassies in Kenya and Tanzania.
Kini was also thought to have been behind an unsuccessful attempt on the life of former Pakistani Prime Minister Benazir Bhutto, who was later killed in a separate attack, US officials said.
The Pakistani official told the BBC the two were trying to develop a weapon that could shoot down the high-flying drone aircraft.
He said he did not know if they were involved in the suicide bombing of the Marriott but he said Kini was certainly behind the bombing of the Danish embassy in Islamabad in June last year.
They were known in South Waziristan as "The Lion" and "Mr Engineer", the official added.
It was reported on 1 January that an unmanned CIA aircraft had fired three missiles in the Karikot area of South Waziristan, killing three suspected militants.
Initial reports suggested those killed were militants of Turkmen origin.
The US has launched dozens of similar drone attacks in recent months, mostly targeting Taleban and al-Qaeda militants in Pakistan's tribal regions.
The lawless tribal areas (Fata) on Pakistan's border with Afghanistan are considered a sanctuary for the insurgents.
The US says the militants regularly cross over the porous border into Afghanistan where the US troops have been fighting since 2001.
The drone attacks are believed to have been largely on-target, hitting Taleban and al-Qaeda hideouts.
There have been few civilian casualties, officials say.
But Pakistani media and opposition parties term these attacks a violation of Pakistan's sovereignty and territorial integrity and the government has been under immense public pressure to defend its territory against them.
Islamabad says the attacks are counter-productive as they help offset the negative popularity the Islamist militants have gained in areas under their control.