The New Haven Police Department lost another top official two weeks ago, leaving embattled Chief Frank Limon with only one of four assistant chief positions filled.

Assistant Chief Thomas Wheeler, one of two assistant chiefs whom Limon brought with him from the Chicago Police Department, announced his retirement March 8, and officially left the NHPD three days later. Wheeler, the third assistant chief to leave since Limon was sworn in in April, was in charge of the Investigative Services Division and left the department for a position in academia, City Hall spokesman Adam Joseph said in a press release. The retirement leaves the NHPD under the sole leadership of Limon and Assistant Chief Tobin Hensgen, even though Limon asked the Board of Aldermen’s Public Safety Committee in early March to fill all four assistant chief positions.

When asked if any assistant chief position would be filled in the near future, NHPD spokesman Joseph Avery told the News, “I don’t know, but I would hope so.”

Avery said that the decision to hire new police leaders falls under the office of City Hall Chief Administrative Officer Robert Smuts ’01, and that the NHPD is not involved in these decisions. Smuts did not respond to requests for comment.

Wheeler’s retirement from the NHPD comes after the departures of Assistant Chief Ariel Melendez and Assistant Chief Stephanie Redding, leaving the department understaffed at the top.

But these departures have yet to have a clear negative impact on the department.

Under Wheeler, solved homicides jumped from under 10 percent through the first quarter of last year to nearly 55 percent by the end of 2010. Although the city’s murder rate rose 84 percent from 2009 to 2010, Limon also saw his department influence a 1 percent reduction in overall crime.

Melendez left the NHPD after 33 years on the force amid multiple controversies. In addition to leading the Oct. 2 raid on the Morse-Stiles Screw at the Elevate nightclub — which a recently released NHPD Internal Affairs report admonished for poor planning and leadership — Melendez was also responsible for ordering an officer to take away a citizen’s video camera, erase the camera’s recorded video and arrest the citizen. An Internal Affairs investigation made public March 3 found that Melendez violated NHPD policy during both of these incidents.

But Melendez retired from the NHPD with a $124,500 annual pension, which exceeded his salary of $105,000. The Board of Aldermen has since sought to readjust the pension plans for the NHPD’s top officials.

Redding, who served in the department for 25 years and twice assumed the role of acting chief during transitional periods, left her post as head of the administrative division in June. She did not give an explicit reason for leaving two months after Limon was sworn in, but she said in June that her decision was “difficult.” Redding also left the department with a pension higher than her salary while on the job.

Soon after Limon was sworn in, he brought Wheeler and Hensgen to the NHPD from his former department in Chicago. After the departure of Melendez, Limon and his two remaining assistant chiefs were villified as the “Chicago Three” by police union leaders.

Following widespread departmental claims of low morale and poor leadership, the NHPD rank and file held a “no confidence” vote against the “Chicago Three.” The 246-to-21 vote was an overwhelming criticism of the NHPD leadership.