Association of Salaried Medical Specialists executive director Ian Powell said the deficits were a reflection of how underfunded the health system was.
He said the expectations on district health boards were increasing much faster than funding.
"It's a pretty untenable situation."
While deficits were wiped by the Ministry of Health at the end of each year, pressure was put on health board leaders to find ways to cut costs and keep within the budget, Powell said.
"That [cutting costs] is the pressure that's on them but it's very difficult to do that without reducing services in some ways."
Powell said better leadership could also help cut costs. He believed more if more specialists were employed, they would have the time to invest in improving hospital systems.
He said without major changes the deficits were only going to get larger in coming years as the health system struggled to meet demand.
Health Minister Jonathan Coleman said despite the deficit no services would be cut.
Keeping deficits under control was an important part of sustaining growth in DHB services, he said, although in every year since health boards were created in 2001/02, at least seven health boards were in the red.
"In 2008/09 National inherited a combined DHB deficit of $155m, with 16 of the 20 DHBs in deficit at around 1.6 per cent of total DHBs funding for the year."
He said this year's $117m deficit was a fraction of the $13 billion district health board budget.
"Services will not be cut - there's plenty of cash in the bank."
Ministry of Health systems outcomes group manager Sam Kunowski said the results were expected to be unfavourable this year and the ministry had agreed to a $58.7m deficit however it turned out to be significantly larger.
