By Laura Zuckerman

(Reuters) - The U.S. Justice Department has opened an investigation into the handling of numerous sexual assault allegations involving students at the University of Montana, where at least two members of the football team are accused of rape.

University President Royce Engstrom told Reuters he was informed of the inquiry during a meeting on Monday with Justice Department officials who told him the probe would examine the response of the Missoula-based university, city police and county prosecutors.

A spate of alleged rapes, the implication of student athletes in some of them, and the abrupt dismissal last month of the football coach and athletic director has shaken the campus and battered the image of a school celebrated for its Big Sky Conference champion football team, the Montana Grizzlies.

Engstrom said it was not made clear to him what prompted the inquiry, nor could he specify its scope, but he cited "a general heightened awareness of sexual assault activity on our campus and community," adding, "It's certainly related to that."

A Justice Department spokeswoman in Washington declined comment, but a law enforcement source said agency officials planned to hold a news conference in Missoula on Tuesday afternoon to discuss the matter.

The handling of sexual assault complaints in college sports programs is getting closer scrutiny in the wake of child sex abuse scandals involving coaches that engulfed Penn State and Syracuse University.

A University of Montana report released in January identified nine alleged student-related sexual assaults or attempted assaults since late 2010, including at least one reported gang rape, and two more sexual assault allegations involving students have surfaced since then.

Criminal charges have been filed so far in just one case under scrutiny -- against Grizzlies' running back Beau Donaldson, who is accused of raping a woman at his residence while she slept following a night of heavy drinking.

Donaldson, who has pleaded not guilty, has been suspended from the team.

In addition to Donaldson, the football team captain and quarterback Jordan Johnson was accused of rape in March and placed under a restraining order granted to his accuser. No charges have been brought and he, too, maintains his innocence.

Johnson was initially suspended, but has since resumed practicing with teammates.

Coach Robin Pflugrad, who had praised Johnson's "tremendous moral fiber" in an interview with the Missoulian newspaper after the case surfaced, was himself unexpectedly let go from the university in March, along with athletic director Jim O'Day.

'CONFUSION ... AND FEAR'

The scandal has angered some and bewildered others in Missoula, a western Montana city of 86,000 whose economy and identity are intertwined with the state's flagship research institution and its alter ego, Griz Nation.

"There is confusion and disappointment, sorrow and fear," Mayor John Engen said in a recent interview with Reuters, summarizing community sentiments.

On the 15,600-student Montana campus, questions are being raised about the behavior of standout athletes.

"Personally, my feeling about this is, what's going on with the football team?" said Brittany Salley-Rains, student and co-director of the university Women's Resource Center. "If there has been some hesitation to hold players involved to the same standards as other students, that's a problem."

What schools like Penn State and the University of Montana have in common are storied football programs deeply ingrained in the fabric of the community, said Norman Pollard, dean of students at Alfred University and researcher behind a national study on hazing among student athletes.

"Allegations of sex crimes paint such a contrasting picture that it's difficult for a community to accept and difficult for the victims to come forward," he said, adding that some victims were treated with suspicion as a result.

Sexual assaults on college students are hardly confined to universities with major sports teams. About 20 percent of young college women will fall victim to attempted or actual sexual assault, according to a 2007 study on campus sexual assault by the National Institute of Justice.

The NIJ study found that college men who participated in aggressive sports in high school, including football and basketball, used more sexual coercion in their college dating relationships than men who did not take part in such athletics.

"Programs can create a culture where it brings out the best in players," Pollard said. "Or they can create a culture where it is winning at all cost, and people's behavior isn't questioned so long as they do well on the field."

(Reporting by Laura Zuckerman in Idaho and Jeremy Pelofsky in Washington; Writing by Steve Gorman; Editing by Cynthia Johnston and Lisa Shumaker)