New Haven Police Department Chief Frank Limon will resign this November after a tough 20 months in the top job.

Mayor John DeStefano Jr. announced Limon’s resignation, effective Nov. 15, at a City Hall press conference Monday afternoon, ending speculation that erupted over the weekend following reports Limon had cleared out his office and local condominium in advance of a trip to Illinois that started Friday. Those reports suggested the chief was not simply on leave to recuperate his health and attend a police conference, but rather making a permanent exit from the department, which he joined last April.

“[The decision was reached] after two weeks of discussions regarding [Limon’s] personal circumstances and goals for the department,” DeStefano said at the press conference, adding that he will announce Limon’s replacement at a press conference 3 p.m. Tuesday.

Since arriving from Chicago, Limon has presided over a 9 percent reduction in the Elm City’s overall crime rate this year, even as New Haven slugs through its deadliest year since 1994 — the homicide count for 2011 sits at 27. Calls for Limon’s departure picked up after the NHPD Union’s Feb. 3 landslide vote of “No Confidence” against him, with members citing departmental mismanagement and inability to connect with rank-and-file officers.

But DeStefano said that Limon’s departure was due to mutual agreement, and that he had no cause to dismiss the chief. Limon will continue his contractual relationship with the department through June 2012 as a consultant, DeStefano said, continuing his initiatives with violence and community intervention. He added that Limon will earn $90,000 during this time, a package that came from discussions these past two weeks.

Even if he wanted to, DeStefano could not have sacked Limon thanks to the city’s charter, which offers job protection to the police chief through his four-year contract unless he commits some criminal activity or egregious offense.

Still, much of Monday’s attention focused on the secrecy behind Limon’s departure. As of Sunday evening, both City Hall spokesman Adam Joseph and NHPD spokesman David Hartman stressed that Limon was still police chief despite his departure. Those claims ran counter to those of mayoral candidate Jeffrey Kerekes and former NHPD union president Sgt. Louis Cavaliere, who said they received multiple reports from officers that Limon’s departure was permanent.

“My concern, like that of a lot of other people, is why the city didn’t handle the information [of Limon’s departure] properly,” said NHPD Union president Arpad Tolnay in an interview Monday before DeStefano’s press conference. “I’m going to step out of a limb and say, if this is a small peek at how politics is conducted here in New Haven, then maybe it’s time to switch things up.”

When asked if his actions amounted to lying, DeStefano replied that he acted as he saw fit. But he said that “speculation had become so rampant” that he felt it would have been a mistake not to announce Limon’s departure today.

Following the press conference, Kerekes said that DeStefano still had some questions to answer regarding the manner of Limon’s departure.

“It’s a credibility issue,” Kerekes said, adding that neither the public nor the Board of Aldermen had a say in selecting the new chief. Kerekes is running to unseat DeStefano in the city’s Nov. 8 mayoral election.

In an interview Sunday night, Kerekes charged that Limon’s departure would be the result of mismanagement starting at City Hall, where DeStefano has gone through six police chiefs in his 18-year tenure because of his tendency to “micro-manage”. DeStefano has caused morale issues within the department because officers are promoted “based on who they know and not what they do,” Kerekes said.

Hartman deferred Monday afternoon to City Hall for comment on the selection of the new chief, explaining that the NHPD does not appoint its new chief.

Ward 12 Alderman Gerald Antunes, who serves as the vice chair of the city’s public safety committee, said the Board of Alderman has not yet been given information about or an opportunity to weigh in on Limon’s replacement. He said his committee had expected the chief to resign for some time, though declined to say how long he has known about the situation.

When asked whether Dean Esserman, a former Providence Police Department chief and NHPD assistant chief, was in contention to replace Limon, Tolnay said he had heard the name discussed. Tolnay added he was unsure about other individuals in the running for the chief’s job.

Current Assistant Chief John Velleca will serve as the department’s acting chief until Limon’s resignation in November.

Yale Police Department Chief Ronnell Higgins said though he was similarly in the dark about who the mayor has picked to run the NHPD, he looks forward to working with Velleca and the new chief. The impact of the new NHPD chief on the YPD’s operations will be minimal, he added.

“When I learned the news [of Limon’s departure], I immediately called the acting chief and stressed our commitment to working with him and he expressed the same back to me,” Higgins said.

Velleca currently heads the NHPD’s investigative services division.