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All district health boards are implementing new rosters as a result of the multi-employer collective agreement covering junior doctors coming into effect.
The rosters should now be in place, but the SDHB is one of 14 health authorities yet to have hired enough doctors to make the new rosters work effectively.
The agreement was settled in February last year, and at that time all DHBs undertook to begin recruiting new junior doctors.
"Dunedin didn't, so they were behind the eight ball in the first instance - about a year behind the eight ball now," association national secretary Deborah Powell said.
"The second thing is that they put their ads on a [web]site where RMOs [resident medical officers] never go, and we found that out and said can they move to RMOs' normal channels, so, hopefully, we will see a reaction."
The new rosters should mean junior doctors will not work more than four consecutive night duties.
The association is charting the progress of each DHB towards completing the new safer rosters.
At the end of January, based on its advocates' assessments, it said just seven of 21 DHBs had finished the new rosters.
Some - such as Counties Manukau and Waitemata - were tracking at just 20%.
The association rated the Southern DHB at 50%.
"It is all very slow and when they do do something, they don't do the right thing," Dr Powell said.
"I'm not saying they are doing it deliberately.
"It's just that not enough care, not enough enthusiasm, not enough energy is going in to it.
"It's all very haphazard, and that's not good enough."
SDHB specialist services executive director Patrick Ng said the organisation welcomed the new rosters but was experiencing the same difficulty as other DHBs finding doctors to fill those roles.
"These are positive changes for both our staff and our patients, as junior doctors will experience improved time to recover between shorter periods of consecutive nights," Mr Ng said.
"The Southern DHB is employing more junior doctors. However, recruitment is taking some time to achieve the numbers we require, and we are working on solutions to fill the rosters in the interim.
"The rosters are being implemented across New Zealand, which means all DHBs are actively recruiting to increase their numbers at the same time, which has placed demand on recruitment across the sector."
Mr Ng said under the new rosters junior doctors were likely to work four nights and then later on three nights - effectively the same amount of nights, but worked at different times.
"We have been working closely with the RDA on roster compliance and we believe their assessment is reasonably accurate," he said.
"We are working hard towards full compliance, which requires us to successfully recruit to fill roster gaps."
Dr Powell said the association was prepared to give DHBs some leeway on rosters last year because of the need to recruit doctors, but DHBs had had the time to find staff and that was no longer acceptable.
Dr Powell said Dunedin Hospital was "fragile", with ongoing issues securing staff in several areas, including emergency and general surgery.
"It's just an overall picture of not getting on to it, and we have to keep on lobbying and pressuring to get it some attention, and it shouldn't have to be that way - it should be front and centre for all DHBs."