The Pentagon's Office of Inspector General is looking into whether CENTCOM officials altered conclusions of intelligence assessments prepared for senior policy makers, including President Barack Obama, to play up progress against the Islamic State.
"The IG has a responsibility to investigate all allegations made and we welcome and support their independent oversight," CentCom said in a statement.
"While we cannot comment on ongoing investigations, we can speak to the process and about the valued contributions of the Intelligence Community (IC). The IC routinely produces a wide range of subjective assessments related to the current security environment."
CENTOM said while the multiple agencies within the intelligence community typically seek input from fellow members on their assessment before publishing them, the primary agency does not have to incorporate that feedback.
However, omitting input from other agencies appears to be a direct violation of government rules, according to Mark Mazzetti and Matt Apuzzo, of the New York Times, who first reported the investigation into CENTCOM.
"Legitimate differences of opinion are common and encouraged among national security officials, so the inspector general's investigation is an unusual move and suggests that the allegations go beyond typical intelligence disputes," the Times reported on Tuesday.
"Government rules state that intelligence assessments 'must not be distorted' by agency agendas or policy views. Analysts are required to cite the sources that back up their conclusions and to acknowledge differing viewpoints."
White House Press Secretary Josh Earnest on Wednesday said President Obama "places a premium" on getting an "unvarnished assessment" from the intelligence community, which he expects to gather multiple viewpoints.
"I can tell you that the President's expectation is that his national security team will work diligently to get information to him and other members of the team that reflects an accurate assessment of what's exactly happening on the ground."
The Obama administration has faced fierce criticism for its strategy against Islamic State. Throughout Washington, assessments about how the campaign is progressing have varied widely, but the administration has maintained that its strategy is working.