St. Paul is pouring $1 million into major changes at its troubled police crime lab, but a key move to boost its scientific credibility could be stalled by an internal fight over union rights.

The St. Paul Police Federation and city officials are at odds about whether a newly created forensic lab manager post violates the federation’s terms and conditions of employment. The job description requires strong scientific training and experience, which favors civilians. A sergeant has historically overseen the lab’s operations.

The federation said in a statement Tuesday that it will take “all legal steps necessary” to address the city’s insistence on hiring a civilian.

“Legally speaking, they have to renegotiate if they want to do that,” said Chris Wachtler, the federation’s attorney.

Sgt. Shay Shackle oversaw the lab from 2001 until last July, when courtroom testimony revealed that lab staff did not follow basic scientific procedures in its drug testing. Independent audits later revealed a host of problems, including poorly maintained testing instruments, unscientific language in reports and deficient skills among staff.

Consultants recommended hiring a scientist to oversee the lab, prompting the creation of the lab manager post. New forensic scientist jobs were also created, but they will replace jobs previously held by civilians who were laid off.

The city’s stance is that the manager job is a new classification that doesn’t violate the federation’s contract, and that no promotional opportunities were lost. Shackle is still a sergeant.

“We have an excellent police department ... but they’re not forensic scientists,” said city labor relations manager, Jason Schmidt. “To me, it would be irresponsible for the city to ignore what the experts recommended we do.”

Federation representatives and Wachtler met with Schmidt and Assistant Chief Kathy Wuorinen on March 7 to discuss the dispute, but a compromise couldn’t be reached. The federation asked the city to renegotiate, and either guarantee that no sworn officers would be required to report to the civilian manager or create a new promotional position for sworn personnel.

“Sworn officers should not be reporting to civilians,” Wachtler said.

Two police sergeants and three officers currently work in the lab, analyzing fingerprints and crime and crash scenes. The lab stopped drug testing last July. As part of the lab’s reformation, the city will fund two positions at the Minnesota Bureau of Criminal Apprehension to test suspected drugs.

The city is seeking accreditation for the police lab. Schmidt said the city can’t earn accreditation without a forensic scientist overseeing the lab.

“The city is really just trying to put the right people in the right positions,” he said.

The federation supports the reform but lacks faith in the city, its statement said.

“It is unfortunate that the city and police department leadership have neglected budget and staffing issues in the crime lab for years,” the statement said. “The issues facing the crime lab in recent months are a direct result of this. Leadership pleading ignorance of these issues and civilianizing the lab’s management will only create more problems.”

The federation has not taken any legal action yet. Wachtler said it is looking at options.