Defense Secretary Ash Carter has asked his under secretary of defense for intelligence to make clear to military officials that the Pentagon chief expects "unvarnished, transparent" intelligence, the Pentagon announced Thursday.

The order was given recently, Pentagon press secretary Peter Cook told reporters during a Pentagon briefing.

"He's made clear that he expects candid intelligence analysis ... for folks to call it like they see it, and that's his expectation," he added. "Unvarnished, transparent intelligence is what this secretary expects on a daily basis."

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It comes after reports that military commanders at U.S. Central Command, which oversees the war against the Islamic State in Iraq and Syria, were altering intelligence assessments to make it seem that the terrorist group and al Qaeda's Syria affiliate were weaker than they were.

More than 50 Defense Intelligence Agency analysts embedded at Centcom support a complaint delivered to the Pentagon inspector general, The Daily Beast reported Wednesday.

In response to the complaint, the inspector general launched a report in July, the New York Times reported. However, the scope of the complaint was a new revelation.

Earlier in the day, the former No. 2 at the CIA said that if there was tampering with the analysts' assessments, heads should roll.

“If there is truth that somebody has been meddling with their analysis, I think somebody needs to lose their job over it,” former CIA deputy director Mike Morell said on CBS's “This Morning.”

Cook, who declined to discuss the investigation so as to not influence its outcome, said it would be best to wait until it finishes before making any judgments on punishment.

He also said Carter still believes the U.S. has the "right strategy" in the war against ISIS in Iraq and Syria, which began last August.

"He has looked at this in a very diligent, deliberate way, and feels strongly that we are moving forward," Cook said.

"He does believe ultimately we're going to prevail," he added. "But he's been candid ... that this is not going to be easy."

- Updated at 3:24 p.m.