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Sarah Gardner has left the organisation while it is under investigation by the Environment Minister and councillors, and tensions between staff and councillors have disrupted business as usual operations.
The council's first female chief executive was said to be a clear stand-out among candidates when she was appointed at the end of 2017.
The resignation was announced in a statement just after 2pm today.
In the statement, Mrs Gardner said leaving the position was something she had been considering for some time.
"It had been an absolute privilege to lead such a special organisation full of talented people who care about their region.
“While often misunderstood, the work of Regional Councils is vital to the future of regions like Otago. Management of natural and physical resources, building resilience to natural hazards and climate change, and facilitating community work for environmental benefit, pest management and landowner led outcomes is imperative for future generations".
Regional council staff are special people who work hard and sacrifice more lucrative careers for the public good, she said.
Otago Regional Council chairman Andrew Noone said Mrs Gardner had made a considerable contribution in her time at ORC.
"We sincerely thank her for all she has done for Otago. She has raised the practice and performance of the organisation in many areas and has been a well-respected and highly thought of CE.
"Her legacy will be evident in several areas, particularly with the strength of the team she has built in the organisation, with the greater role Council is playing in projects making a difference on the ground across Otago, with the fit for purpose freshwater policy in progress and in the exciting new headquarters development that the organisation expects to relocate to next year.
"Mrs Gardner will be sorely missed and we wish her every success for her future.”
Mrs Gardner leaves the council on May 18.