The US attorney general has acknowledged four US citizens have been killed in drone strikes since 2011.
In a letter to the Senate judiciary committee, Eric Holder defended the targeted killing of Anwar al-Awlaki.
But he said Awlaki's 16-year-old son as well as two other individuals were "not specifically targeted by the US".
The disclosure comes as President Barack Obama prepares to make a speech on counter-terrorism and the drone programme on Thursday.
A White House official quoted by Reuters said the US president would discuss why the use of drones was "necessary, legal and just".
The disclosure of the killings in Yemen and Pakistan marks the first formal public acknowledgement of the US citizen deaths in drone strikes.
"The president has directed me to disclose certain information that until now has been properly classified," Holder wrote.
America's top law enforcement official defended the killing of Awlaki, whom he described as a "senior operational leader" of al-Qaeda in the Arabian Peninsula (AQAP).
Holder said Awlaki was "intimately involved in detailed planning and putting in place plots against US persons".
Holder added officials "appropriately concluded that [Awlaki] posed a continuing and imminent threat" to the US.
Awlaki, who was born in the US state of New Mexico, was killed in a missile strike from an unmanned plane in Yemen in September 2011. US officials announced his death but did not officially reveal he was killed by a drone.
Samir Khan, a naturalised US citizen who produced an online magazine promoting al-Qaeda's ideology, died in the same missile strike.
Awlaki's 16-year-old son Abdulrahman, who was born in Colorado, was killed in Yemen a month later.
Jude Kenan Mohammad, a North Carolina resident with a Pakistani father and an American-born mother, was arrested in Pakistan in 2008 after trying to enter a part of the country that is dominated by militants and is off-limits to foreigners.
He was charged with weapons possession and lacking the correct paperwork but disappeared after being granted bail.
According to his acquaintances, Mohammad is thought to have died in a strike in November 2011 in Pakistan's South Waziristan region, the New York Times reported.
Claims of transparency
Speculation of his death had been reported in local media in Raleigh, North Carolina, where he lived, but was not confirmed by US officials before Wednesday.
President Obama is due to give a speech on national security later on Thursday.
"He will discuss why the use of drone strikes is necessary, legal, and just, while addressing the various issues raised by our use of targeted action," the White House official said.
Also on Thursday, the president is expected to sign a "presidential policy guidance" detailing when the US can use drones.
Holder said the Obama administration had been transparent with Congress over its policy on drone strikes.
He cited an unclassified paper the justice department provided to congressmen that outlined the legal justification for the attacks.
In that document and in a speech at Northwestern University in March 2012, Holder said strikes against US citizens could only be justified if the person posed an imminent threat of violent attack against the US, could not be captured, and the strike was conducted in a way that was consistent with the laws of war.