MISSOULA, Mont. -

NBC Montana has confirmed that a third investigation has been launched at the University of Montana.

This time, the university?s football program is under investigation for alleged but unspecified violations.

It is just the latest development for the university, which is already under separate investigations by the U.S. Department of Education and the U.S. Justice Department over allegations of how the school handled sex assault allegations involving students.

The National Collegiate Athletic Association has refused to confirm or deny whether it had launched an investigation.

But, after a specific request to the Montana Board of Regents Wednesday, university leaders decided to ?make public the fact an investigation is under way.?

The UM gave NBC Montana a letter from the NCAA, addressed to University President Royce Engstrom. It is dated January 30, 2012.

The letter asks the school to not discuss the investigation.

But Montana Associate Commissioner of Higher Education Kevin McRae writes in a statement, ?In consultation today with the NCAA, and at the request of KECI, the University leadership has decided to make public the fact that an investigation is under way.?

McRae says the decision was made in the interest of responsiveness and transparency.

The NCAA letter orders athletes, employees and administrators to fully comply with the investigation.

McRae says, "We're fully supportive of and aware of the NCAA bylaws and guidelines for the investigation and cooperating with the NCAA in response to their questions and information requests."

The letter is signed by NCAA Vice President of Enforcement, Julie Roe Lach.

It outlines steps the NCAA investigation will take and says it is possible the review could extend beyond the football program to other university programs.

Investigators can close the case if they find no evidence of wrong doing.

But, if they do, the investigation is then referred to the Committee on Infractions. That step would lead to hearings where the University of Montana could face possible sanctions.

To read the response NBC Montana received from Kevin McRae on behalf of Royce Engstrom, click here.

To read the notification sent to UM by the NCAA, click here.