The Finance Minister says the junior doctors' strike is more about hours than money - but is refusing to say if he thinks they're working too much.

Junior doctors have begun their 48-hour strike over working conditions.

The strike will see thousands of people miss out on surgery today and tomorrow as 80 per cent of junior doctors walk off the job.

A second 48-hour strike is also planned for January 29-30.

Some junior doctors on strike say they've been forced to work 16-hour days and believe their working conditions could jeopardise patient care.

Speaking with Newstalk ZB, Finance Minister Grant Robertson told Tim Dower patients need to know they're being cared for by someone who's thinking clearly.

But he said those who work in the health industry know it's unique.

"If people were working 16-hours a day, every day of that week that wouldn't be possible and that isn't what I understand resident doctors do."

"[But] within the health system, people know that it's a 24/7 system, that it operates through the night and people understand that from time to time you will work long shifts."

When asked whether it was okay for a public entity, like the District Health Boards, to expect people to work for 16-hours a day, Robertson said, "these are clinical decisions and I won't comment as a politician".

"Clearly we all want the people who are looking after us in our hospitals to be working in safe environments, to be in a position to be making good decisions and clearly, that's what marks a health system that is safe and working well for people. Clearly, we want that.

"Those decisions about what the exact number of hours are that people can work, what the balance is between getting the right training you need and having a healthy working environment is exactly what's being debated between the two groups."

He said his main priority is to make sure New Zealanders have a safe and professional health system.

"I am not going to debate the individual ins and outs of this deal."

"What I want is to make sure that New Zealander's have a health system that is staffed by professionals, that are well trained and who are able to do their job properly, and we are encouraging the DHBs and the resident doctors to come to an agreement about that."

District Health Boards spokesman Dr Peter Bramley told Tim Dower DHBs are committed to looking after the junior doctors.

"This is about shaping the best training experience but also shaping the working rosters to enable us to deliver the right care to the right people in the right place."

"Our first commitment is to patient care, the second commitment is to making sure our employees are working in safe conditions..where there are plenty of limits to ensure safe rostering is still in place but we are wanting some greater flexibility that allows [us] to configure the rosters to deliver better care."

Bramley told Newstalk ZB the main sticking point for the DHBs is flexibility over rosters.

"At a local level, at a particular service level, the one size fits all approach to rostering actually isn't working and if they can have local decision making in conjunction with the RMOs [Resident Medical Officer] then we can get a better training experience."

He hit back at claims that the DHB wants to "have it all", saying RMOs will be consulted about their rosters.

"We are committed firstly to looming after them as employees. We are committed to safe care as DHBs but actually, RMOs are in training and they do move around and it's that want to move around between hospitals in a planned way that enhances their training opportunities."

Bramley said the key issue of the strike isn't relayed to money or pay negotiations.

"We haven't really talked about the money. I don't think money fundamentally is at the heart of this."

"The issue around how we are supporting and working with our RMOs in delivering care is the key issue at stake."