"This was a screw-up that could have been disastrous," the president said during the meeting in the White House situation room, according to the White House media office.
"We dodged a bullet but just barely. It was averted by brave individuals, not because the system worked, and that is not acceptable," he told them.
In a televised statement after the meeting, Obama said "it is increasingly clear that intelligence was not fully analysed or fully leveraged".
"That's not acceptable and I will not tolerate it."
Obama's comments came after Robert Gibbs, the White House spokesman, told reporters that Umar Farouk Abdulmutallab, the Nigerian arrested over the failed bombing, had given intelligence to US officials just hours after his arrest on December 25.
"[Abdulmutallab] was taken from the plane in Detroit. FBI interrogators spent quite some time with him," Gibbs told reporters.
"I don't want to get into all the specifics, but I think they would agree he has provided - in those interrogations - useful intelligence."
Abdulmutallab was allowed to board a plane in both Lagos and Amsterdam despite US intelligence agencies and the state department having received information that many critics have said should have seen him placed on a so-called "no-fly" list.
Bob Ayers, a former US intelligence officer, said Obama's announcement was an attempt to "correct the perception that he's being soft on national security".
"It provides him with an opportunity to demonstrate that he's concerned and he's tough and he's going to do something about this problem," Ayers told Al Jazeera.
But Ayers also warned against blaming the incident solely on the failure of the US intelligence process.
"The man still had to go through a security checkpoint. He was allowed on to an aircraft at his point of debarkation without even having a passport.
"That's not an intelligence failure, that's an airport security failure."
Obama said the system of so-called watch lists of potential suspects would be reviewed in light of the attempted attack.
Analyst tells Al Jazeera Obama's criticism of intelligence agencies is 'somewhat misleading'
In the wake of the 9/11 attacks in New York and Washington, the FBI and other US agencies drew up lists intended to prevent suspected criminals or people labelled terrorists from boarding flights to and within the US.
The "watch list" comprises 550,000 names of people who US authorities believe have possible ties to terrorism but do not present a specific threat and are allowed to fly.
The much smaller "no-fly" list comprises about 4,000 people who the US claims present a known, specific or suspected threat to aviation.
US authorities have already imposed stricter screening regulations for US-bound airline passengers from Yemen, Nigeria and 12 other countries, including possible full-body pat-downs, searches of carry-on bags, and full-body scanning.
But the "enhanced screening" rules got off to a patchy start, amid complaints of delays and discrimination.
Several European governments, including Germany, France and Spain, said they were still studying the rules before implementing them.
Meanwhile, in the Netherlands, Dutch investigators said they found no evidence to suggest Abdulmutallab had contacted accomplices at an airport in Amsterdam.
Officials said he underwent a security interview and check and did nothing unusual in his three-hour stopover.
"Investigations so far have uncovered no indication that the suspect contacted possible accomplices at Schiphol, left the transfer area or behaved suspiciously," the national prosecutor's office said in a statement.
"At the moment, it appears that he was already in possession of the explosives before he reached Schiphol."