In two of the seven rosters at Tauranga hospital, resident doctors work up to 12 days in a row, which includes some 16-hour day shifts, and up to seven consecutive 10-hour night shifts.
He said patient safety could be compromised when doctors were suffering from fatigue.
He said workmates at the end of 12-day shifts were so tired they were "desperate to get out of hospital".
Mr Ellis said it was hard to understand why district health boards had not allowed the changes to the two rosters, or offered an alternative.
Both the Bay of Plenty DHB and the Ministry of Health directed questions to a statement from Whanganui DHB Julie Patterson, lead CEO for the 20 DHBs' Workforce and Employment Relations Programme.
It was released after a mediation meeting on Monday between the DHBs and the NZ Resident Doctors Association failed to make progress.
The statement said New Zealand offered some of the best working hours in the world for doctors, but there was still a need, in some services, to reduce the hours they work.
"By the union's own admission the DHBs have thus far dealt with 80 of the 144 rosters where the union has raised as a concern.''
Mrs Patterson said DHBs were being asked to accept a premise that rostering RMOs for fewer days and out-of-hours work, without a corresponding reduction in pay, would somehow result in better public health services.
"DHBs will not accept this premise."
She said the DHBs had made an offer that undertook to review all rosters of concern, with an offer of a 5 per cent pay increase for resident medical officers over the next three years.
In a statement, NZRDA National Secretary Dr Deborah Powell said while the DHBs had accepted the concerns as genuine, they were only prepared to address the issue of seven consecutive night shifts.
"The DHBs said they could move to no more than four consecutive 10-hour night shifts over the next two years, but were not prepared to address the 12 consecutive day shift rosters."
"Whilst at least a step in the right direction, making doctors safer at night but not during the day fails way short of what is needed to keep doctors and patients safe."
New Zealand Nurses Organisation industrial adviser for the DHB sector Lesley Harry said the district health boards needed to take doctor's concerns seriously.
"This is a major red-flag safety alert for doctors and their patients," she said.
"Nurses can testify that what doctors are saying about short staffing and burnout is a fact. I think the public don't want to have that person treating their loved ones in a life-or-death situation."
What Worksafe says
Worksafe New Zealand was unable to comment on the specific rosters, but stated the Health and Safety at Work Act requires businesses to have the "primary responsibility for the health and safety of their workers, and any other workers they influence or direct."
