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He won by more than 500 votes over his nearest rival, businessman Jeff Hill, while sitting mayor Malcolm Macpherson polled the lowest of the three candidates.
Mr Lepper (54) is a company director, of Earnscleugh, who has been a Central Otago District Councillor for 21 years.
Dr Macpherson had served three terms as mayor.
Preliminary results: Tony Lepper, 2959. Jeff Hill 2410, Malcolm MacPherson 2343.
The Central Otago District Council was elected unopposed. It is: Stephen Battrick, Graeme Bell, Martin McPherson, Neil Gillespie, Terry Emmitt, Gordon Stewart, Tony Lepper, Clair Higginson, Barry Becker, John Lane, John Kerr.
For Central Otago community board results click here