HOOKSETT — The town’s police chief resigned Thursday after years of controversy. The resignation of Stephen Agrafiotis comes at the end of a lengthy paid administrative leave and after an audit that revealed significant turmoil within the police department.

Police Commissioner Clark Karolian confirmed that the commission accepted Agrafiotis’ resignation during its Thursday night meeting. Karolian said Capt. Jon Daigle, who took over as acting chief on Sept. 22, would continue to serve as chief. Karolian did not offer any further details on how the department would fill the position and he would not discuss the resignation further.

“Chief Agrafiotis was a long-time employee of the Hooksett Police Department. The Commission respects his decision to resign at this time, and wishes him the best in the future,” the commission announced Friday in a short press release.

Agrafiotis did not return a call for comment.

Neither Police Commission chairman Joanne McHugh nor Karolian returned calls requesting information regarding whether Agrafiotis was provided a severance package. Town Administrator Dean Shankle said that the former chief’s weekly salary was $2,032.80, which he continued to receive while on leave. That amount would equate to about $36,000 of pay since Daigle took over as acting chief.

Agrafiotis had been placed on leave previously in 2005 during a labor relations-related investigation. The results of that investigation were never made available. He was also at the center of controversy during the 2009 firing of school resource officer Jay Defina. After the town rallied in support of Defina, he was given his job back in September 2010. In 2005, Defina was one of a group of officers who signed a letter of no confidence against Agrafiotis. Defina, along with former Hooksett officer Gregory Martakos, have filed lawsuits against the town and the former chief.

The resignation comes as the police commission and department are working toward improving the department. Public Safety Strategies Group of West Townsend, Mass., which performed the department’s audit, presented its findings in November detailing what needs improvement. The group cited a lack of communication between the chief and department, which led to widespread distrust throughout the ranks.

The audit group has been hired for another year to help the department implement the recommendations. Kym Craven, Public Safety Strategies Group’s director, said the group will continue to help the commission and department and will continue its monthly reports on the progress made.

“We are continuing our service to the town and the commission,” Craven said. “We will provide an update every month on what is going on.”

The press release states that Agrafiotis submitted his resignation Jan. 31.