(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. 
What is the investigation's focus?
systemic issues