The District Health Boards say they are happy to cut down the long stretches junior doctors work, but want some flexibility in negotiations.
More than 3000 doctors walked off the job at 7am on Tuesday to protest long working hours, safe working conditions and pay.
The doctors are asking for the maximum number of days they work in a row to be cut from 12 to 10, and the number of night shifts in a row reduced from seven to four.
DHB spokeswoman Julie Patterson is disappointed the strike is going ahead.
"I think the union is picking out the worst of their conditions and only talking about them.
"The union hasn't moved one iota since the first of March."
Ms Patterson says the DHBs are happy to cut down the long stretches junior doctors are currently working, however they are not prepared to pay them for days they don't work, as the doctors are asking.
The national secretary of the Resident Doctors' Association (RDA) Dr Deborah Powell says the strike comes after years of lobbying for better conditions.
"After four years of trying to get this done we want something more certain than just a commitment - we want a contractual obligation."
She says the reason for the strike is ultimately the issue of patient safety.
"The second thing is that the District Health Board have said it will take two years to do this, we don't think that is necessary so there is a time frame issue in there, and then the third thing is to make sure the time they do get off is meaningful."
The RDA says it is aware the changes would be more expensive as the workforce would need to grow to cover the lost hours.
But Dr Powell says it will be worth it for a better workforce.
"It is a cost but we've acknowledged that...but we believe the health and safety of the doctors and their patients is worth it though. We've got the doctors to do this."
How DHBs will cope with the strike
DHBs around the country say they are well prepared for the next 48 hours without junior doctors.
The country's 20 DHBs are asking Kiwis to visit their GP for minor injuries, with hospitals likely to bear the brunt of industrial action.
DHB industrial action planner, Anne Aitcheson, says they have had time to prepare.
"Over the last two weeks, since notice of action has been received, each DHB has had a team looking at re-rostering staff and altering the level of services we provide."
Some non-urgent appointments and operations have been rescheduled because of the strike, while senior doctors are demanding $568 per hour for covering the strike by their junior counterparts.
Ms Aitcheson is confident acute patients in hospital and those who are admitted on Tuesday and Wednesday will be well looked after.
Meanwhile Health Minister Jonathan Coleman is not taking sides on the issue, instead saying it's an employment dispute between the DHBs and their workers.
"I think it's very important that the junior doctor workforce is treated fairly and has safe conditions and is remunerated well, but the issues are quite complex and negotiators on both sides are working through them."
Dr Coleman says he wants the issues resolved quickly.
"I'm very keen obviously to make sure that we get the people of New Zealand the services that they need and to that we need a fully engaged junior doctor workforce which is back to work as soon as possible."