The US Central Intelligence Agency has been operating a secret airbase for unmanned drones in Saudi Arabia for the past two years.
The facility was established to hunt for members of al-Qaeda in the Arabian Peninsula, which is based in Yemen.
A drone flown from there was used in September 2011 to kill Anwar al-Awlaki, a US-born cleric who was alleged to be AQAP's external operations chief.
US media have known of its existence since then, but have not reported it.
Senior government officials had said they were concerned that disclosure would undermine operations against AQAP, as well as potentially damage counter-terrorism collaboration with Saudi Arabia.
The US military pulled out virtually all of its troops from Saudi Arabia in 2003, having stationed between 5,000 and 10,000 troops in the Gulf kingdom after the 1991 Gulf war. Only personnel from the United States Military Training Mission (USMTM) officially remain.
The Washington Post reported that President Barack Obama's counter-terrorism adviser, John Brennan, a former CIA station chief in Saudi Arabia, played a key role in negotiations with the government in Riyadh over building the drone base.
Senators are expected to ask Mr Brennan about drone strikes, the memo and the killing of Awlaki when he faces a confirmation hearing on his nomination to become the new CIA director on Thursday.
The location of the secret drone base was not revealed in the US reports.
However, construction was ordered after a December 2009 cruise missile strike in Yemen, according to the New York Times.
It was the first strike ordered by the Obama administration, and ended in disaster, with dozens of civilians, including women and children, killed.
US officials told the newspaper that the first time the CIA used the secret facility was to kill Awlaki.
Since then, the CIA has been "given the mission of hunting and killing 'high-value targets' in Yemen" - the leaders of AQAP who government lawyers had determined posed a direct threat to the US - the officials added.
The New York Times published its report on Tuesday night, ending an "informal arrangement" among several news organisations not to disclose the location of the base.
News organisations had been complying with a request from Obama administration officials, who said it might undermine operations and collaboration with Saudi Arabia, the Washington Post reported.
Two other Americans, including Awlaki's 16-year-old son, have also been killed in US strikes in Yemen, which can reportedly be launched without the permission of the country's government.
Kristian Coates-Ulrichsen, an expert on Gulf politics at the London School of Economics, told the BBC that Saudi anxieties about the growing threat of AQAP would have been behind the government's decision to allow the US to fly drones from inside the kingdom.
"The Saudis see AQAP as a very real threat to their domestic security," he said. "They are worried about attacks on their energy infrastructure and on the royal family, so it fit their strategy to allow the drone attacks."
The existence of the base was likely a "sensitive issue" for both Washington and Riyadh, Mr Coates-Ulrichsen added.
A source close to the Saudi Interior Minister, Prince Mohammed bin Nayef, declined to comment when contacted by the BBC.
Saudi Arabia is home to some of Islam's holiest sites and the deployment of US forces there was seen as a historic betrayal by many Islamists, notably the late leader of al-Qaeda, Osama Bin Laden.
It was one of the main reasons given by the Saudi-born militant to justify violence against the US and its allies.
The revelation of the drone base came shortly after the leaking of a US justice department memo detailing the Obama administration's case for killing any American abroad who is accused of being a "senior, operational leader" of al-Qaeda or its allies.
Lethal force is lawful if they are deemed to pose an "imminent threat" and their capture is not feasible, the memo says.
The threat does not have to be based on intelligence about a specific attack, since such actions are being "continually" planned by al-Qaeda, it adds.
NBC News said it was given to members of the US Senate intelligence and judiciary committees as a summary of a classified memo on the targeted killings of US citizens prepared by the justice department.
The latter memo was written before the drone strike that killed Awlaki.
Under President Obama, the US has expanded its use of drones to kill hundreds of al-Qaeda suspects in Pakistan, Afghanistan and Yemen. It says it is acting in self-defence in accordance with international law.
Critics argue the drone strikes amount to execution without trial and cause many civilian casualties.