Doc this week confirmed its restructure, which cuts 72 full-time jobs nationwide and reduces its 11 conservancies into six new ''conservation delivery'' regions.
Under the new structure, which will take effect in September, Otago is absorbed into the Eastern South Island and Southern South Island regions.
The restructure also creates two teams nationwide, one doing field work, ''conservation services'', and the other developing new conservation initiatives ''in partnership with other organisations''.
Doc deputy director-general Doris Johnston said additional government funding meant 60 front-line jobs had been added to the restructure.
Two management layers had been replaced by one, supported by senior rangers, she said.
Otago's Dunedin-based conservator and area manager positions had gone, as had the area manager positions based in Alexandra, Wanaka and Queenstown.
Instead, those offices would be headed by conservation service managers and conservation partnership managers.
In Otago, those who worked in conservation partnerships would come under the South and Eastern South Island region, while front-line staff in conservation services in Oamaru, Dunedin and Taiaroa Head would be in the Eastern South Island region.
Otago's other offices would fall in the Southern South Island Conservation Services region.
Of the newly-created 12 top regional jobs, called conservation services directors and partnership directors, a partnership director will be based in Dunedin and a conservation service director in Invercargill.
In Dunedin, that meant 15.5 staff were allocated to conservation services and 14 to partnerships, including a national tenure review manager, making up 29.5 full-time positions.
Of the 54 positions to be based in Invercargill, 46.5 were allocated to conservation services and 7.5 to partnerships, including an iwi consultation position.
Figures released by Doc showed Otago had 124 full-time positions (13 of those vacant) and it proposed to reduce numbers to 103. However, in the final restructure, it added another five positions, bringing the total to 108.
As a result, job cuts in Wanaka were reduced from four to two, Queenstown retained its current 19 jobs and Clyde and Owaka each got one more position than proposed.
Alexandra's proposed losses stayed the same (five) while staff numbers in Oamaru increased by one as proposed, Macraes Flat stayed the same at three and Taiaroa Head at two.
Glenorchy and Dunedin each lost one more position than proposed.
In Southland, the restructure resulted in six position losses, six fewer than first proposed. Invercargill gained an extra three positions while Te Anau lost six, four fewer than proposed, and Stewart Island lost three, two more than proposed.
