The Missoula County Attorney’s Office will change the way it responds to reports of sexual assaults under an agreement announced Tuesday that ends a federal investigation into whether gender bias played a role in deciding whether to prosecute rape cases.

The changes will include training prosecutors, treating assault victims better, boosting investigation techniques and improving data tracking, communication and coordination, U.S. Department of Justice officials said.

The agreement is the last piece in an investigation into the University of Montana, the city of Missoula and the county attorney’s office. The probe began in 2012, two years before the May 1 disclosure that 55 colleges and universities nationwide are facing similar federal Title IX investigations.

The Montana investigation found evidence of gender discrimination in the way the county attorney’s office handled sexual-assault complaints. Prosecutors were not adequately trained for sexual-assault cases, gave those cases a low priority, often treated victims disrespectfully and did not provide support for victims.

“What we are saying (is) the county attorney’s office lacked the system and infrastructure necessary to enable them to make a decision on whether to prosecute sexual-assault complaints,” Acting Assistant U.S. Attorney General Jocelyn Samuels told The Associated Press.

Missoula County Attorney Fred Van Valkenburg disputed the findings and filed a lawsuit alleging the Justice Department had no authority to investigate his office. The deal announced Tuesday ends that dispute and calls for Van Valkenburg to drop his lawsuit.

It also designates the Montana attorney general’s office to oversee the development and implementation of the county’s new standards and procedures. The attorney general will review the sexual-assault cases the Missoula attorney’s office declines to prosecute.  

The county attorney’s office also will hire a former sex-crimes prosecutor as an adviser to provide training and make recommendations on the new procedures.

Montana Attorney General Tim Fox said in a statement Tuesday that he and Van Valkenburg entered into an agreement separate from the Justice Department on how the changes will be made.

In the federal agreement, Fox, Van Valkenburg and the county denied any laws were broken and continued to say the Justice Department had no jurisdiction or authority to investigate the county attorney’s office.

“Montana law is clear: My office has the authority and responsibility in this matter,” Fox said.

But the Montana officials set the disagreement aside to focus on promoting justice and treating assault victims “in a caring and nondiscriminatory manner,” he said.

Van Valkenburg called the federal claims “utterly unfair” but said it’s more important to end the dispute and “get on with the business of proving to everyone that the dedicated professionals in the Missoula County Attorney’s Office do as good a job or better of handling sexual assault cases.”

Samuels said she was confident in the Justice Department’s jurisdiction, but the agreement does not second-guess any of Van Valkenburg’s past decisions or intrude on prosecutorial discretion.

The Montana probe included a review of more than 350 reports of sexual assaults in Missoula between 2008 and 2012. It found that in some cases, women were led to believe the assaults were their fault or that reports were not properly investigated.

The university, city and Missoula Police Department reached separate settlements last year, and U.S. Attorney Michael Cotter said improvements have been made in responding to sexual assaults since then.

Van Valkenburg is retiring when his term is up at the beginning of 2015.