(CNN) -- The mayor of a Montana college town Wednesday welcomed a federal investigation into allegations that sexual assault and rape complaints were improperly handled.
But John Engen, mayor since 2006, was also surprised when he was notified of the probe.
"This is uncharted territory for us," he told CNN.
The U.S. Justice Department announced Tuesday it was launching a probe into allegations that up to 80 complaints of sexual assault over three years were not investigated thoroughly because of gender bias. Of those, 11 cases involved students at the University of Montana -- at least two involving football players.
"If Justice has enough information that it believes an investigation is warranted, I'm not going to question that," Engen said. "Clearly they have a responsibility to act on whatever complaints they are hearing. I think time will tell whether this was the right call or not."
Assistant Attorney General Thomas Perez of the Justice Department's Civil Rights Division said the focus of the investigation was not on the number of reported allegations, but on the response.
"Our focus is on systemic issues; that is, do the university and the law enforcement agencies have the necessary policies and practices in place to protect women in a comprehensive and integrated manner," Perez said at a news conference Tuesday.
The Department of Education is coordinating with Justice officials, a spokesman told CNN.
Fred Van Valkenburg, Missoula County chief prosecutor, vehemently defended his office and the police officers involved in the investigations.
"We adamantly deny that we have done any such thing, and we are deeply disturbed with the allegation that we have done so," he told reporters.
"I do not believe there is any reason to think that anyone at UM is violating anyone's constitutional rights," he said. "We have not been told even in the most minimal fashion what it is we have allegedly done wrong. We are left to speculate what allegations are being made."
Perez defended the Justice investigation, saying that it was the only way to determine whether there has been any wrongdoing.
"There are a lot of women in this community and a lot of stakeholders in this community who have strong concerns right now," he said.
In December, the University of Montana initiated its own investigation after allegations of a female student being gang-raped and possibly drugged by other students. The university hired Montana Supreme Court Justice Diane Barz to investigate, and she looked into nine alleged sexual assaults from September 2010 through December.
Barz wrote in her report that the university has "a problem of sexual assault on and off campus."
That report triggered a preliminary review by the Justice Department, which resulted in the investigation.
Engen said Perez notified him last Thursday and met him and other officials involved Tuesday morning before the announcement.
At least 11 allegations of sexual assault involving students were reported in the last 18 months. And at least two of the allegations are said to involve football players on the University of Montana Grizzlies football team.
"As to the university, we are investigating whether it responds promptly and effectively to allegations of sexual assault and harassment on campus and has taken the necessary steps to combat sexual violence," Perez said.
University of Montana President Royce Engstrom said the school was "fully committed to cooperating and collaborating in this investigation. We have taken this matter extremely seriously from day one."
Engen said the Penn State child sex abuse scandal changed the way many people think about campus incidents.
"Missoula is no Penn State," he said. "But I think we are like a lot of places. Our experience is not unique."
In March, the university dismissed football coach Robin Pflugrad and athletic director Jim O'Day. University officials gave no specific reason -- only that it was time for new leadership.
But students reacted, some with anger.
Andrew Fink wrote on a university Facebook page that the administration was to blame -- not the coach and the athletic director.
"I'm glad I'm not a Grizzly anymore! You hold Robin Pflugrad responsible for the sexual assaults on campus? How despicable! These men should be accountable for their own actions!"
Jason Woodill wrote that the university's handling of sexual assaults on campus was a joke.
"The way the U of M has handled the sexual assaults makes me ashamed to be a student. The level (of) incompetency is blatant and ludicrous," he wrote on Facebook.
Missoula, a city of about 68,000 people in western Montana, is closely linked to the school. The University of Montana is the top employer in the city, and many local professionals are alumni.
The city of Missoula recently launched a campaign called "It's Your Call -- 911" to encourage victims of sexual assault and rape to come forward.
The city police website now has extensive information answering this question: "What will happen if I contact the Missoula Police Department about being sexually assaulted?"
"I think there has been an expectation that as a community, we ramp up our efforts," Engen said. "Ultimately as mayor, my responsibility is to the broader public, its safety and welfare. I want justice done."