Airport manager Sean Flynn has been placed on administrative leave with pay, following a Friday morning closed-door session with the Martha’s Vineyard Airport Commission.

The decision to place the embattled manager on leave was confirmed by commission chairman Myron Garfinkle at the conclusion of the 45-minute executive session. Mr. Garfinkle said the meeting was called to “discuss the reputation, character, physical condition or mental health, rather than professional competence, of an individual, or to discuss the discipline or dismissal” of an employee. Mr. Flynn has been on the sidelines since August 10 when he began an unscheduled vacation. At the time Mr. Garfinkle said the manager would not return to work, that the airport commission was negotiating an amicable separation agreement and that a search would begin for Mr. Flynn’s successor. But with no apparent successful outcome to the mediation talks, the airport commission on Friday morning took formal steps as outlined in Mr. Flynn’s contract.

Mr. Flynn was present for the meeting with his attorney. The airport commission was represented by its Cambridge attorney David Mackey.

The commission is now following a disciplinary procedure outlined in the contract. The commission must give Mr. Flynn 30 days advance notice of any vote to terminate his contract; additionally, the manager is entitled to a hearing before an independent hearing officer, and the right to formally respond to any decision that emerges from that hearing.

Mr. Flynn has served as airport manager since 2005. In February, the airport commission renewed his contract for three years, effective July 1, at a starting annual salary of $138,822. The new contract calls for cost of living increases, and a two per cent raise in each successive year of the agreement, based on a positive annual performance review.

Commission voted to go into executive session. — Steve Myrick

His base salary at the beginning of his previous five-year contract, signed in 2010, was $115,756, with similar provisions for cost of living adjustments and annual raises.

While under his previous five-year contract, the airport commission could terminate Mr. Flynn for cause by majority vote, the current contract adds detail to the process.

Mr. Flynn is entitled to a detailed accounting of the nature of the grounds for cause 30 days before any vote on termination, along with the opportunity to rectify any deficiencies during that time. He has the right to a hearing before an impartial hearing officer 10 days in advance of any vote to terminate his contract.

Where cause was defined in the previous contract as a material breach of his contract, willful or gross neglect of his duties, or engaging in conduct that was “materially injurious to the airport,” the new three-year contract expands the definition of cause to include any admission or conviction of a misdemeanor materially or adversely affecting the airport commission, conviction on any felony charge, fraud, or misappropriation of airport property.

Also spelled out in the new contract are some additional rights for Mr. Flynn, including the right to be represented by a lawyer at a hearing, to exchange copies of evidence and witness lists with the airport commission at least 48 hours in advance of a hearing, and to formally respond to any findings of a hearing officer.

The new contract also includes provisions for regular working evaluations of Mr. Flynn’s job performance by the personnel subcommittee of the airport commission, and detailed provisions prohibiting the manager from disclosing confidential airport information, during his employment, or after termination for any reason.

The new contract was approved by the airport commission in a 5-2 vote in February of this year. Former commissioners Constance Teixeira and James Coyne, who voted for the contract renewal, were replaced a month later by the Dukes County Commission, which appoints the airport board. A third commissioner who voted in favor of the new contract, Denys Wortman, did not seek reappointment.

Of the seven airport commissioners serving in March 2014, six had been ousted by the county commission by March 2015, during a contentious year in which the two boards sued each other in superior court and clashed repeatedly over control of airport operations.

Mr. Flynn’s management style and job performance have been criticized in recent years. He, along with the airport commission and the county commission are the subject of an ongoing workplace discrimination lawsuit filed by a former employee. On June 18, 2014, Mr. Flynn was granted an eight-week medical leave of absence.

This summer, Mr. Garfinkle and airport commission vice chairman Robert Rosenbaum told the Gazette that following a scheduled inspection and follow up surprise inspection, the FAA raised questions and demanded action on several issues involving airport operations. The FAA said failure to quickly correct the deficiencies could result in a loss of the airport’s license to operate as a commercial facility.

The airport commission and the FAA have declined to provide copies of the FAA inspection reports or other communications with Mr. Flynn, citing an ongoing FAA investigation.