Prosecutors have charged University of Montana quarterback Jordan Johnson with rape Tuesday who became the second member of the team to face such charges amid investigations by U.S. authorities into the handling of sexual assault reports by school and local officials.

Jordan Johnson, 20, was formally charged with sexual intercourse without consent, Missoula County District Attorney Fred Van Valkenberg said in a written statement.

According to an affidavit filed by prosecutors, the charges stem from accusations by an unidentified fellow student, that Johnson raped her in her bedroom on February 4 after she invited him to her room to watch a movie.

Johnson has previously denied the allegation. "Jordan strongly maintains his innocence and looks forward to the opportunity to prove his innocence at trial, clear his name and return to pursuing his education," Johnson's attorney, David Paoli, said in a statement.

He also added the family members and friends of Jordan are 'surprised and saddened' by the timing of the criminal charges since the encounter took place in February and police have been aware of the allegation since the woman filed a report six weeks later.

As of now, Jordan has been suspended from the football team activities as per the student athlete conduct code pending the charges. University President Royce Engstorm has confirmed the suspension.

Speaking for the university, Kevin McRae, Montana's associate commissioner of higher education, said the school has no basis for expelling Johnson, who has not yet been convicted of a crime and is registered to attend classes in fall.

"The university will be a very interested observer of the district court proceeding to see how the due process plays out," McRae wrote in an email to Reuters.

This is the latest development in the sexual assault scandal at the University that has prompted three investigations by federal agencies and the NCAA. Earlier this year, running back Beau Donaldson was suspended from the team after he was charged with raping an acquaintance in September 2010.

The sexual assault allegations and investigations have shaken Missoula, a city of 86,000 whose identity and economy are tied to the university and its football team.