Martha’s Vineyard Airport manager Sean Flynn is leaving his job, the chairman of airport commission said on Thursday, capping months of tension over operational issues and workplace disputes.

“We’re negotiating an amicable separation,” commission chairman Myron Garfinkle told the Gazette. “We hope it will be concluded within the next two weeks.”

Mr. Flynn, who began an unscheduled two-week vacation last week, will not return to work, Mr. Garfinkle said. Assistant airport manager Deborah Potter “has assumed day-to-day responsibilities” and will continue to do so, he said.

A formal search for a new airport manager will follow, he added.

Mr. Flynn has served as airport manager since 2005. This February, the airport commission renewed his contract for three years at an annual salary of $138,822, a 20 per cent increase over the salary set in 2010 when he signed a five-year contract. Three of the five commissioners who voted for the contract were replaced the following month.

His departure ends a 10-year career that in recent years has been marred by controversy over his management style, including a lawsuit alleging workplace harassment by a female employee. More recently, Mr. Flynn came under fire for his handling of a routine inspection conducted in May by the Federal Aviation Administration.

He could not immediately be reached for comment Thursday.

At an airport commission meeting last week, Mr. Garfinkle said he and vice chairman Robert Rosenbaum had met with officials from the FAA and the Massachusetts Department of Transportation to discuss the results of the inspection. The officials identified four areas of concern: a wildlife management plan, plans for a new safety building, poor employee performance and inadequate runway markings. Two of the areas triggered a noncompliance status, the wildlife management plan and runway markings issue. According to Mr. Rosenbaum, officials said they had had difficulty resolving the issues with airport management, a situation he characterized as “highly unusual.”

On Friday, August 7, commissioners met in executive session to consider an unspecified non-union employee matter. On the following Monday, Mr. Flynn left for a two-week unscheduled vacation.

At the commission meeting last week, Mr. Garfinkle said the airport is under an Oct. 15 deadline to correct deficiencies identified by the FAA or face loss of millions of dollars in federal grant money and potentially its certification as a commercial airport.

Mr. Flynn was criticized at a May 28 commission meeting by Mr. Rosenbaum and another commissioner, Rich Michelson, for not advising commissioners that the inspection was taking place and for excluding them from an exit briefing.

Mr. Michelson described how after he and Mr. Rosenbaum asked to be included in the exit briefing with FAA inspectors, Mr. Flynn abruptly moved the meeting from a conference room into his office.

“So when I walked in, Sean said, ‘No, Rich,’ and I said, ‘No what, Sean?’ And he said, ‘You are not invited to this meeting. This is a private meeting.’ So I said to him, ‘Okay, Sean, so there are two airport commissioners here who would like to attend this meeting and you are refusing us access to that meeting. Is that correct?’ And he said yes,” Mr. Michelson said.

Mr. Rosenbaum added, “I thought the treatment was rather inappropriate and disrespectful for commissioners. I thought that was a very poor way, in front of employees and the FAA inspectors, to deal with that.”

Mr. Flynn, who was present at the May 28 meeting, offered no comment to the criticism from Mr. Rosenbaum and Mr. Michelson. Earlier in the meeting, when asked about the inspection results, he said, “It was a successful inspection. We did find more things than we’re usually used to. Most of them are paperwork in nature.”

Even before the FAA inspection, relations between the airport manager and some new members of the commission had been strained, stemming from their appointment by the Dukes County Commission. At odds with the airport commission for years over control of the airport, county commissioners in March ousted two members of the seven-member airport commission and appointed Mr. Garfinkle, Mr. Rosenbaum and Clarence (Trip) Barnes 3rd.

For two months following the new appointments, Mr. Flynn refused to schedule monthly meetings of the commission, citing legal concerns about the validity of the appointments. On May 21, commissioners called their own meeting, and elected Mr. Garfinkle chairman and Mr. Rosenbaum vice chairman. Mr. Flynn did not attend that meeting. The May 28 meeting when the FAA inspection was discussed was his first meeting with the newly-constituted commission.

Since then, a personnel committee headed by Mr. Rosenbaum has been working on new personnel policies. At a meeting several weeks ago, the committee voted to hire a human resources consulting firm to assist in the process. Though Mr. Flynn attended that meeting, he later filed an open meeting law complaint, claiming it was improperly held. The commission plans respond to the meeting complaint in September.

In February 2014, a female airport employee filed a complaint against Mr. Flynn and others alleging sexual harassment and workplace retaliation.

In the past week, Mr. Garfinkle and Mr. Rosenbaum have been meeting regularly with assistant airport manager Deborah Potter, who is heading airport operations in Mr. Flynn’s absence. This week, they attended a staff meeting with the operations team that Mr. Garfinkle described as “upbeat” and “very well received.” He said the staff is dedicated to rectifying the issues and hopes to exceed the minimum requirements during next year’s annual FAA inspection.