A new report released Thursday found nearly 3,500 untested rape kits are sitting on shelves in police departments' evidence rooms. But law enforcement agencies reported they had legitimate reasons for choosing not to process the kits.

After rape, hospitals collect evidence in kits and send them to law enforcement. Investigators then determine if the kit should be processed by the Minnesota Bureau of Criminal Apprehension for DNA.

A national controversy over the number of untested rape kits prompted Minnesota legislators to pass a law that requires all police departments and sheriff's offices to count the number of untested kits and explain why they're there.

The report released Thursday by the BCA tallied up those numbers and found 3,482 untested sexual assault kits from offenses dating back to the 1990s. The Duluth Police Department has the most with 578, followed by Anoka County Sheriff's Office with 495. St. Cloud reported 306 and Rochester reported 145.

State Rep. Dan Schoen, DFL-Cottage Grove, who authored the rape kit bill, said the total number seems high, but isn't surprising. The discussion should be around whether or not police have kits that should've been tested but weren't.

"If there are agencies out there that have kits on the shelves, whether it's one, two or whatever, and there is a victim who deserved justice that didn't get it," he said, "we've got a problem."

Reasons police gave the BCA for having untested kits varied. They included ongoing investigations, victims choosing not to participate in the criminal investigation and "other."

That "other" category, which accounted for 983 untested kits, listed a number of additional reasons from each department like insufficient evidence, conflicting statements, closed cases and dismissed charges.

Statewide, law enforcement reported 738 kits were untested under the "prosecution declined" category.

"Would the DNA test have helped make the decision on whether they should prosecute or not?" asked Schoen, who has worked as a police officer. "I don't know. That'll be information we need to find out."

The BCA report also found 1,056 kits were untested because the "victim did not participate" which could mean a variety of things, too. Some choose to get exams but do not file a police report. Or they may file a report, only to decide later not to go forward.

Laura Taken-Holtze, spokesperson for the Minnesota Coalition Against Sexual Assault, said there shouldn't be a "mad rush to get everything tested."

"If a victim wants that then yes, absolutely," she said. "But if they don't, then they shouldn't be forced to have their kit tested when they've already been through the trauma of a rape."

The Minneapolis Police Department reported 194 untested rape kits in Thursday's report. But as a response to an MPR data request in August, the department said it had 509.

Lt. Mike Sauro, who worked for the sex crime unit and was in charge of the research, said about half the kits don't have a corresponding police report and therefore cannot even be processed for DNA extraction. He said guidelines prevent police from putting the sample into the national DNA database without a suspect being investigated.

"You don't want your finger prints being entered into the national database if you haven't committed a crime," he said. "It's a personal privacy rights issue."

The Minneapolis Police Department chose not to report those numbers to the BCA because the labs wouldn't take those kits for testing anyway.

"Theoretically it's kind of a no man's land," Sauro said. "And that was our interpretation."

The BCA report also said 25 law enforcement agencies did not report their count at all and it's not clear why they didn't participate. Schoen called it a "great error in judgement."

"It makes it look like there is some sort of nefarious activity on their part," he said.

Lawmakers will have to decide what to do now that they have this data. In its report, the BCA estimated it would cost the state $4.4 million to test all of the kits internally. It would cost between $2.4 and $5.5 million to contract with private labs, the bureau said.

It's not clear yet what policy changes could result from this audit. Currently, each law enforcement agency has its own policies. The St. Paul Police Department has had a policy in place for the past five years that requires mandatory testing of all rape kits.

Sauro said it's possible the state would enforce new policies that take the discretion out of investigators' hands, which he said is not a good idea.

"These investigators are highly trained, highly experienced," he said. "They know the parameters of when a kit should be tested or not. I don't like that discretion to be taken away from them."

BCA officials say there has been a 39 percent increase in rape kit submissions for testing in 2015 over 2014. The turnaround time will likely surpass 60 days. The report also said the BCA lab has its own backlog of 157 untested kits.