The Newton police chief’s former secretary was charged with larceny Tuesday in allegedly stealing $660 from the department, in a case that has roiled the law enforcement agency.

A Framingham District Court magistrate issued a complaint against Jeanne Sweeney Mooney on one count of felony larceny over $250 after a court hearing, according to Police Chief Matthew Cummings and Mooney’s lawyer, Thomas Drechsler.

Mooney, who had worked for the Newton Police Department for more than 30 years, has been on paid administrative leave since last September.

She plans to plead not guilty at her arraignment, probably next month, Drechsler said.

Mooney contends that the police pursued the charges against her in retaliation after she began civil action against the department, her lawyer said. “There is more than reasonable doubt here,” he said.

In May, Mooney sent a letter to the the city demanding $600,000 in damages from Newton for pain and suffering stemming from the allegations, as well as reinstatement in her job and the firing of Cummings.

Mooney was placed on leave after police said a witness saw her take an envelope containing cash collected through various police permit fees, according to her letter. She was also accused of destroying nearly $1,500 in checks, the letter said.

In the letter, Mooney alleged that Cummings verbally humiliated her on two occasions and tried to intimidate her into taking on more responsibilities. The letter also says Mooney complained that Cummings gained an 8 percent raise without following proper protocol.

The city hired an outside investigator to look into Mooney’s allegations against Cummings. That report is scheduled to be completed at the end of August.