Mrs Patterson admitted the strike would impact on the board's ability to met health targets set by the Government.
"We've lost five days now, two days last strike and three days this strike.
"It will affect our elective service performance, but we're pretty confident that, with careful planning and the rescheduling, we will stay SV compliant.
"Prior to the strike - and nothing to do with the strike - we had a problem with neurology with waiting times and this has just made it a little bit worse."
If the health board doesn't meet health targets, there can be financial penalties imposed by the Ministry of Health.
The strike is about the association's campaign for safer working hours, but Mrs Patterson said its demands had been met.
"The union claims revolved around what they claimed to be health and safety issues," she said. "The 20 health boards agreed to meet all demands around those claims, but that still hasn't satisfied the union."
She said New Zealand junior doctors now had the best working conditions and pay in the western world.
She said the association was trying to control how rosters were organised, something unacceptable to health boards, but she believed negotiations would be successful.