MISSOULA — The University of Montana announced Thursday that it has removed the interim tag from football coach Mick Delaney’s title and given him a two-year deal to lead an embattled program caught up in an investigation of how the university as a whole handled allegations of sexual assault. 

Delaney was chosen as the interim head coach for the 2012 season after coach Robin Pflugrad was relieved of his duties in March and told his contract wouldn’t be renewed. Interim athletic director Jean Gee said Delaney’s new contract expires in January 2014.

Gee said Delaney brings expertise, mentorship, leadership and integrity to the job — and said giving him the permanent post removes “a cloud of uncertainty” hanging over the program.

Delaney said he expects the Grizzlies, a perennial Football Championship Subdivision playoff contender, to keep winning despite an ongoing NCAA investigation that comes amid federal scrutiny over the way the university handled sexual assault complaints.

Delaney, a Butte native, said he does not believe the heavy NCAA sanctions imposed on Penn State portend bad things for his program. 

“There is no comparison between what happened at Penn State and what the NCAA is looking at here,” he said.

The U.S. Department of Justice is investigating whether the university, campus police and Missoula police and prosecutors improperly handled reports of rape and sexual assault, including allegations involving football players. The Department of Education also is looking into a sexual discrimination complaint filed in January that named the football program.

School officials announced in May that the NCAA had opened an investigation into the program, but have not disclosed what the investigation involves.

Delaney’s hiring comes as university President Royce Engstrom continues to shake up his cabinet-level positions. Engstrom said he decided recently that Delaney was the right person for the job after watching the way he has handled the program as the interim coach.

Engstrom called the hiring a “big step,” and said recruits and fans needed a permanent coach to bring stability and direction to the program.

“This is a time to look toward a strong and vibrant future for Grizzly Athletics,” Engstrom said. 

Delaney said the team has not lost any recruits so far because of the cloud hanging over the school. 

“I can guarantee you we will recruit kids of high character, Number One” he said. “We don’t have the time or resources to chase around guys that don’t do the right things.”

He said academics would be the second priority in recruiting, followed by athletes who can “play a little bit, too.”

“Our young men know they are under so much scrutiny right now, they are being watched 100 percent of the time,” Delaney said.

Expectations remain high despite the off-field troubles.

The Grizzlies have appeared in the FCS, previously Division I-AA, championship game seven times since 1995 — winning it twice. They have won the Big Sky Conference title 11 out of the last 12 seasons. 

Last season, Montana advanced to the semifinals after uncharacteristically missing the playoffs the previous year.

Delaney, 70, said he has plenty of energy for a job he expects will wrap up his coaching career. 

Delaney had been a Montana assistant coach for the past four seasons. Before that, he was an assistant coach at Colorado State for 15 seasons and a head coach at Montana Western of the NAIA in the early 1990s.