US special forces were sent to Syria this summer in an attempt to rescue US hostages, including journalist James Foley, but the secret raid failed.
Administration officials said the team found, after a fight with Islamist militants, that the hostages had already been moved.
News of the raid followed the release of a gruesome propaganda video by Islamic State (IS) militants that showed Mr Foley being beheaded.
The US meanwhile launched a new barrage of airstrikes against Islamic State targets in Iraq on Wednesday, despite the militants' threats to execute another hostage.
The recent rescue mission was authorised after intelligence agencies believed they had identified the location inside Syria where the hostages were being held.
Militants have also threatened to kill Steven Sotloff Officials had also become convinced that "these hostages were in danger with each passing day", Lisa Monaco, Mr Obama's senior counterterrorism adviser, said in a statement.
"The US government had what we believed was sufficient intelligence, and when the opportunity presented itself, the President authorised the Department of Defense to move aggressively to recover our citizens," Ms Monaco said.
"Unfortunately, that mission was ultimately not successful because the hostages were not present."
Several dozen special operations forces were dropped by aircraft into Syria and engaged in a fight with members of the Sunni militant group.
As they fought their way toward the spot where the hostages were believed to be kept, the US forces realised there were no captives to rescue.
Several militants were killed in the gunfight, administration officials said. No Americans died but an aircraft came under fire and one American sustained a minor injury.
The New York Times said the raid targeted an oil refinery in northern Syria and was carried out by two dozen Delta Force commandos.
The newspaper quoted a Defense Department official as saying missing the hostages may have been "a matter of hours, perhaps a day or two".
James Foley disappeared in Syria in November 2012. Pic: Nicole Tung News of the beheading of Mr Foley, a 40-year-old American, shocked the public opinion. President Barack Obama and officials around the Western world have expressed revulsion.
The disclosure of the rescue mission marks the first time the US has acknowledged that American military personnel have been on the ground in Syria since a civil war there broke out more than three years ago.
Caitlin Hayden, spokeswoman for the White House National Security Council, said the administration never intended to disclose the mission but was forced to do so because a number of media outlets were preparing to report on it.
Pentagon spokesman Rear Admiral John Kirby said: "As we have said repeatedly, the United States government is committed to the safety and well-being of its citizens, particularly those suffering in captivity.
"In this case, we put the best of the United States military in harm's way to try and bring our citizens home."
IS, an offshoot of al Qaeda that operates in Syria and Iraq, has warned that another captured American, Steven Sotloff, would also be killed unless the US called off airstrikes in Iraq.
But the US has conducted 14 fresh airstrikes, bringing to 84 the number of such attacks since they began on August 8.
James Foley's younger brother Michael has criticised the US government, saying he thought it could have done more to save Mr Foley.
He said that, as a result, it needed to do more to free Mr Sotloff.
The US officials have not specified how many Americans are believed to be held captive.
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