Dr Angela Pitchford, of Christchurch, finished last week, commissioner Kathy Grant announced.
Dr Pitchford declined to be interviewed.
Mrs Grant said Dr Pitchford had been unable to commit to the full commissioner term, which was extended by three years to expire at the 2019 local body elections.
Dr Pitchford is highly regarded in the sector and has a national role in emergency department services for the Ministry of Health.
But she has maintained a low profile as deputy commissioner.
Mrs Grant said she was unable to confirm whether Dr Pitchford's replacement would be an Otago-Southland clinician.
''[But] I appreciate that there would be significant benefits if that were the case.''
Mrs Grant was unable to say when the new deputy would be appointed.
Information released earlier this year under the Official Information Act showed Dr Pitchford claimed for just 18 days' work as a deputy commissioner between last November 17 and May 17, this year.
During that time the four-member commissioner team ran up $159,600 in daily fees and $25,405 for travel, accommodation and food.
Mrs Grant, who receives the biggest daily fee, $1400, charged for 55.5 days, a total of $77,700.
Dr Pitchford claimed the least number of days, but had the biggest expenses bill ($9272) of the team.
Deputy commissioners Richard Thomson and Graham Crombie had charged 32.5 and 40.5 days respectively.
The deputy commissioners receive $900 per day, as charged.
