New information about the intelligence available in the immediate aftermath of the Benghazi attack raises questions about whether the former No. 2 at the CIA downplayed or dismissed reporting from his own people in Libya that it was a coordinated attack and not an out-of-control protest over an anti-Islam video.

Then-Deputy Director Mike Morell, whose own agency lost two employees at Benghazi, former Navy Seals Ty Woods and Glen Doherty, was heavily involved in editing the administration’s internal narrative on what happened – known as the “talking points” – which served as the basis for then-U.N. Ambassador Susan Rice’s controversial claims about a protest on the Sunday talk shows after the attack.

According to the bipartisan Senate Intelligence Committee report on Benghazi, on Sept. 15, four days after the attack and one day before Rice’s appearance, the CIA's most senior operative on the ground in Libya emailed Morell and others at the agency that the attack was "not/not an escalation of protests."

Fox News has confirmed that three days earlier, the CIA Chief of Station and the agency's team in Libya also sent situation reports, known as sitreps, to Washington.The raw intelligence reporting described a coordinated attack by extremists, not an out-of-control protest.

"In a crisis like Benghazi, you would expect it's going directly to the seventh floor," Sam Faddis, who recently retired from the CIA and writes extensively about the intelligence community, said. The “seventh floor” refers to CIA leadership – at the time, Director David Petraeus and his second-in-command Morell, among others. "In a situation like this, you're going to be looking at it immediately ... your aides are going to be asked to flag it to your attention the second that it comes in and bring it to your desk -- right in front of you," he said.

Further, Fox News has learned new details about a secure video teleconference some 72 hours after the attack.Two sources familiar with the call say it included Morell, the CIA chief of station and Benghazi survivors who were evacuated to Germany -- as well as Greg Hicks, the late Ambassador Chris Stevens' deputy.

Fox News is told that after an update from personnel on the ground, Washington's singular focus on the video left participants in Libya baffled, angry and dismayed that Morell seemed to dismiss their on-the-ground reporting.

On Sept. 12, based on the intelligence disseminated to senior lawmakers, House Intelligence Committee Chairman Mike Rogers, R-Mich., also told Fox News that Benghazi was a “coordinated, military style commando-type” attack.

In a brief statement to Fox News, Morell did not address the situation reports. Separately, Bill Harlow, who is working with Morell on a book, said there was early intelligence reporting from the CIA operation in Libya of a protest before the assault.

This claim conflicts with the assessment of Republican Sen. Richard Burr, who sits on the Senate Intelligence Committee, which recently released a bipartisan report concluding the Benghazi attack was preventable.

Burr said investigators never found credible reporting linking the attack to a demonstration spawned by an anti-Islam video.

"We've done a forensic on that event. We've never found a reference to demonstrations from individuals who were on the ground -- whether it's the chief of station in Tripoli, whether it's the diplomatic security, or the GRS (Global Response Staff) that went ... from day one, all referrals were an attack that was underway that continued well into the night and to the (CIA) annex."

Yet on Sept. 14 -- when the bodies of Stevens, Foreign Service officer Sean Smith, as well as Woods and Doherty, were flown to Andrews Air Force base – then-Secretary of State Hillary Clinton continued to talk about the video.

"We've seen the heavy assault on our post in Benghazi that took the lives of those brave men,"Clinton told the somber gathering."We've seen rage and violence directed at American embassies over an awful internet video that we had nothing do to with."

The video was linked to protests elsewhere in the region. But on Sept. 15, in what appears to be a direct response to the administration's public statements about the cause of the attack, the CIA's chief of station sent the email to Morell saying protests were not involved in Benghazi.

Faddis said it was unusual for the chief of station to directly e-mail the deputy director, but it appeared to be an effort to cut through the bureaucracy, to be sure nothing was getting lost in translation. And by taking the message outside standard intelligence channels, it may have been an effort by the chief of station to allow Morell and others to save face.

"The way the agency works, he's (chief of station), been running 24 hour a day to nail every fact,” he said, “… and now he is reaching out four days into this directly to the most senior levels of his organization, saying again with the big red crayon as clearly as he can, ‘there were no protests, I am trying to do my job and tell you at the most senior level don't go forward with anything that says something we can't factually support’."

Documents released by the administration last May show that by Sept. 15, Morell was engaged on the talking points with the State Department and White House.The bipartisan Senate report shows that on the same day, Morell cut half the text including prior intelligence warnings to the State Department.The word "Islamic" was dropped, but "demonstrations" stayed in.

Harlow said Morell was not aware Rice – or any administration official – was going to use the talking points, adding Morell believed they were being prepared for lawmakers. After the Sept. 15 e-mail, Harlow said Morell asked the chief of station to provide more information, adding that on Sept. 16, the chief of station's response was forwarded to the agency analysts.

"Morell immediately passed that to the analysts who produced the original analysis and asked for their reaction,"Harlow explained. "They responded that they had contradictory information and stuck with their judgment. It wasn't until several days later that the CIA was able to get their hands on the CCTV video (Sept. 18) -- when they did, it was clear there were no demonstrations and the analysts changed their reporting."

This emphasis on the analysts who are thousands of miles from the scene of the attack versus the agency personnel on the ground in Libya does not feel right, according to Faddis and other former intelligence officials contacted by Fox News.

"When I hear that explanation, the words that come to mind are disingenuous and frankly incomprehensible," Faddis said. "This strikes me as -- what you're doing is you're looking for an excuse for not paying attention to what (the chief of station) said."

Since retiring from the CIA last year, Morell has taken on high-profile assignments for the administration, including the NSA review panel, which formulated recommendations for President Obama. In addition to the book deal, he is now a TV commentator on national security issues for CBS News and has taken a position for Beacon Global Strategies, which was founded by Philippe Reines.The New York Times magazine recently described Reines as Clinton's "principal gatekeeper."

In a series of questions via e-mail, Fox News asked Morell for his recollection of the early intelligence, the video teleconference and whether he notified the administration at any point that its public statements were in direct conflict with the reporting of U.S. personnel on the ground in Libya.

While not disputing he was aware of the situation reports and participated in the video teleconference, Morell said: "I stand behind what I have said to you and testified to Congress about the talking point issue. Neither the Agency, the analysts, nor I cooked the books in any way."

While Morell has a standing invitation to speak with Fox News on camera, in his statement he said he does "not intend to get into an extended dialogue with you on the subject nor do I intend to grant you an interview on this matter."

While the bipartisan Senate report speculated that protests elsewhere over the anti-Islam video may have played a role in inspiring the attack, the report concludes the intelligence analysts stayed with the protest explanation for too long.“Analysts inaccurately referred to the presence of a protest at the Mission facility before the attack based on open source information and limited intelligence, but without sufficient intelligence or eyewitness statements to corroborate that assertion. The IC (Intelligence Community) took too long to correct these erroneous reports, which caused confusion and influenced the public statements of policymakers."

In an addendum to the bipartisan Senate report, six Republicans on the committee concluded of the talking points: “Rather than simply provide Congress with the best intelligence and on the ground assessments, the administration chose to try to frame the story in a way that minimized any connection to terrorism.”