Bill Boehm was employed by the former council and still had 18 months left on his contract, but instead will finish on May 31.

Flinders Island mayor Annie Revie made the announcement on Monday.

"Although Mr Boehm has 18 months still to run on his contract, a change in personal circumstances means that he is unable to make the necessary long-term commitment," she said.

"He understands and supports council's need to seek a general manager who can make such a commitment."

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Cr Revie said the "largely new" council had spent the past few months reviewing the strategic approach to maximise the potential of the community over the next four-year period and beyond.

"As part of this review it was noted that a number of significant improvements had been achieved over the past two-and-a-half years under the current general manager," she said.

Cr Revie said Mr Boehm had restored staff and councillor relationships following a challenging staff change, which was critical towards the organisation moving on.

He also initiated some positive operational improvements, implemented changes to the region's rating system, oversaw the development of a sound, long-term financial management plan and secured Building Better Regions funding for the Telstra Communications and Structural Review Projects.

"One of Bill's most timely projects has been to initiate a review of Flinders Business, Economics and Social Structure. The recently released report augers well for the economic and social development of the municipality, as we move into the period of working with our community on a futuristic strategic plan," Cr Revie said.

The mayor said in order to capitalise on the gains the council must now "seek the certainty and continuity of a general manager who can support the council through the strategic planning and, importantly, implementation period".

Mr Boehm said he, and his partner Kaye, had enjoyed their time on Flinders Island and remained passionate about the community.

"I feel we are leaving council in a better place and very much look forward to staying in touch. We will closely follow Flinders' assured strategic growth," he said.

Cr Revie thanked Mr Boehm for his contributions.

"Bill has been a passionate champion of Flinders and leaves with our full support and best wishes," she said.

The council's accountant, Heidi Marshall will act in the general manager's role until a permanent appointment can be made.

Ms Marshall had been a integral part of Mr Boehm's team, Cr Revie said.

"Her knowledge and vast international experience, working at the highest levels in corporations and with government, make her the immediate and obvious choice to act in the General Manager's role through this transition period. The quality of Heidi's work is respected by staff and councillors alike," she said.

"Council extends to Heidi the warmest welcome and looks forward to continuing the already strong working relationship."

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