That classified assessment was broadly consistent with President Obama’s statements on the campaign trail, as he won re-election by pointing to the assassination of Osama bin Laden and claiming that al-Qaida was on the run.

But senior U.S. intelligence officials, including Defense Intelligence Agency Director Gen. Michael Flynn, vigorously objected to that claim and won a partial victory by securing removal of the judgment on al-Qaida.

 “Flynn and others at the time made it clear they would not go along with that kind of assessment,” a U.S. intelligence officer who worked on the al-Qaida file told The Daily Beast’s Eli Lake.  “It was basically: ‘Over my dead body.’ ”

Press reports said that Flynn, who announced his retirement last month, was forced to depart because of  numerous policy disagreements with the Obama administration.

But Flynn and his colleagues were successful in getting the administration to soften its tone.

In his 2012 State of the Union address, Obama declared  that “al-Qaida operatives who remain are scrambling, knowing that they can’t escape the reach of the United States of America.”

But since then, the terrorist group has appeared to be thriving across the Islamic world. In the past two years, it has established safe havens in Iraq, Libya and Syria and carried out scores of lethal, high-profile attacks there and nations such as Afghanistan, Algeria, Egypt, Kenya, Lebanon, Nigeria and Pakistan.

The White House backed down from its upbeat assessment and conceded that al-Qaida remained a serious threat.

Earlier this week, FBI Director James Comey, who took office last year, admitted that he had underestimated the danger posed by al-Qaida affiliates.

"I didn’t have anywhere near the appreciation I got after I came into this job just how virulent those affiliates had become," he told The New York Times, saying that al-Qaida-linked groups in the Middle East and Africa are a greater threat than he had been led to believe.

Comey said he now sees terrorism as the FBI’s primary focus.

Sen. Dianne Feinstein, chairwoman of the Senate Select Committee on Intelligence, told CNN on Sunday that “terror is not down in the world. It is up, both deaths, injuries, in many, many different places. Al-Qaida has metastasized.”

According to the California Democrat, the key question “becomes how do we prevent an attack in this country?”

But tension nonetheless continues between the White House and senior military and intelligence officials wary of an administration they still suspect is seeking to minimize the danger posed by jihadist terrorism.

One senior U.S. intelligence official expressed frustration over what he regards as White House pressure to play down the threat from some al-Qaida affiliates.

“It comes from the top. It’s the message that al-Qaida is all these small franchise groups and they are not coordinated and threatening,” the official said, adding that the administration is wary of expending resources against “something they don’t think is a problem.”

U.S. intelligence officers claim the White House is using wildly outdated figures to understate the size of al-Qaida forces in Kunar province, a  critical battleground  in Afghanistan .

Some in the intelligence community see the deadly September 11, 2012, Benghazi attack as “a similar downplaying” of the jihadist threat, according to The Daily Beast.

“U.S. intelligence officers in Libya on the night of the attacks cabled back that it was a coordinated terrorist attack, only to see Obama administration officials cling to out-of-date talking points that described it as a demonstration gone awry,” the website reported.

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