A troubled Northland council is losing its mayor only a third way through his term and now faces a byelection costing about $38,000.

Kaipara District Mayor Greg Gent announced this week he was resigning due to personal reasons, just one year and one day after he won the 2016 election.

Mr Gent become the first elected leader in Kaipara since the Government sacked the previous council in 2012 and put in a three-man commission to run the troubled district.

Read more: Kaipara mayor announces his surprise resignation

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At the time the challenges facing the council, said to be "beyond the current councillors' ability to resolve", included an $80 million debt arising from the controversial Mangawhai wastewater scheme, legal challenges and governance issues.

Mr Gent told the Northern Advocate he would not elaborate further on why he was leaving, but agreed his resignation was "unexpected".

He will resign on November 14, after which deputy mayor Peter Wethey will carry out the role until a new mayor is elected on February 17.

That is the first available date for a byelection, in keeping with electoral law time frames for nominations, posting ballots and other procedures, and allowing time for Christmas and holiday closures. The closing date for nominations will be Friday, December 22.

The byelection will cost about $38,000, Kaipara's democratic services manager Sean Mahoney said.

Now facing the loss of the first mayor it has been allowed to have in years, and only a third of the way through his term, the council has had four chief executives in five years.

The current acting chief executive, Peter Tynan, was appointed a month ago, after being recommended for the job by Mr Gent.

The appointment followed the sudden resignation in late August of Graham Sibery, who was just over a year into the job. Mr Sibery was appointed by commissioners John Robertson, Richard Booth and Peter Winder ahead of the 2016 elections.

He replaced acting chief executive Jill McPherson who held the role after professional accountant Steve Ruru resigned in October 2014.

The KDC was named by the Taxpayers' Union in August this year as having the highest paid council staff in New Zealand. The union's annual local government league table showed 19 per cent of Kaipara staff were paid annual salaries over $100,000.

On a per ratepayer basis, Kaipara also had the highest total operating costs and the highest debt in Northland, the union said. There are about 15,500 voters in Kaipara.