The top medical role has been vacant since June, when Dr David Tulloch left.
A letter this week from the senior doctors' union, the Association of Salaried Medical Specialists, to chief executive Carole Heatly, obtained by the Otago Daily Times, says the board risks a ''disastrous'' outcome if it bungles the process.
The application period has been extended because of concern about a lack of promotion of the role internally.
It has not been advertised externally, and some staff missed the in-house advertisements.
Extending the time period did not address all of the concerns, association executive director Ian Powell's letter says.
Medical staff had not been invited to select a member of the appointment committee, which was their right under their employment agreement.
A response from Ms Heatly to concerns raised formally by the general medical staff in Otago had been ''disappointing'' because it minimised the issue, the letter said.
Many senior doctors believed the appointment process had been ''constructed'' to ensure a particular outcome.
''The [chief medical officer] position will fail if the appointee does not have the confidence of both the chief executive and senior medical staff,'' Mr Powell said.
''Quite simply, Southern DHB can't afford to get this decision wrong because it could undermine the credibility of both the CMO position and the commissioner ...
''Either, let alone both, would be disastrous for the DHB's future.''
A spokeswoman for Ms Heatly said she was considering her response to the letter. When contacted, Mr Powell said he was looking forward to discussing the matter with Ms Heatly to find a resolution.
