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Acting chief executive Ruth Kibble confirmed on Wednesday Pragati Gautama had handed in her notice and would be leaving in early June.
Dr Gautama was appointed in late November 2018 and moved into the job fulltime in late January last year.
At the time she said the role would "be a challenge" — one she welcomed, given her background in rural medicine.
In an emailed response to questions form the Otago Daily Times, Mrs Kibble said Dr Gautama had resigned for "valid personal reasons", but would not elaborate further.
Waitaki District Health Services chairman Paul Allison said Dr Gautama’s departure was due to "personal family reasons", which meant she had to return to the UK.
Meanwhile, Mrs Kibble rejected speculation the hospital’s last fulltime doctor had left, and that the hospital was completely reliant on locums.
"This is not correct. One doctor has finished this week, however we have three FTE doctors working clinically," she said.
"We are recruiting and have interviewed and are in negotiations with a number of individuals. Yes we are currently negotiating with a number of doctors, but we are not in a position to stipulate a timeframe to be fully staffed.
"The balance of the shifts are covered by locum doctors so that we can maintain services of high clinical quality to our community."
She said a reliance on locum doctors was "not ideal from a financial perspective", and added that other rural hospitals faced the same issue.
"If we look across rural hospitals in New Zealand, there is a estimated shortage of 88 doctors, registrars and nurse practitioners nationally."
Mrs Kibble declined to comment when asked how much the company spent on locum doctors each week.
She would also not comment when asked how many staff had left in the past 12 months, a number the ODT understands to be about 40.
However, she said the company had identified "only two professional groups that are hard to recruit locally", those being "medical and physiotherapy".
Mr Allison announced on February 11 the company had started the recruitment process for a permanent chief executive.
Mrs Kibble was seconded from her role as primary health partnerships director at the South Canterbury District Health Board in September 2018, after the departure of former chief executive Robert Gonzales.