More than 50 U.S. intelligence analysts have formally complained that their reports on terror groups, including ISIS and Al Qaeda, were inappropriately altered by senior officials to fit a narrative that the U.S. is doing better in the war on terror, according to The Daily Beast.

James Rosen reported on "The Kelly File" that top advisors to President Obama have confirmed that the Pentagon is investigating allegations that damaging internal intelligence assessments of the sluggish fight against ISIS and other terror groups are being sanitized on their way up the chain to the commander-in-chief.

"All of this recalls allegations from the past decade about President Bush and Vice President Cheney allegedly manipulating WMD intelligence in the run-up to the Iraq War," Rosen said. "However, the blue-ribbon panel formed to investigate those allegations reported in its final report in 2005 that those claims were unfounded."

Lt. Col. Tony Shaffer (Ret.) told Megyn Kelly there are three areas of intelligence being manipulated, according to his sources.

He said those areas are inaccurate battle damage assessments, overly positive conclusions and the deletion of suggested targets of attacks in the reports.

"This is all a travesty," Shaffer stated.

Watch more above.