About half the country's junior doctors have walked off the job for 25 hours with every aspect of the hospital system likely to be affected.
Te Whatu Ora says emergency departments will remain open and patients should turn up to their regular appointments unless they hear otherwise.
About 2500 junior doctors were due to walk off the job from 7am on Tuesday to 8am on Wednesday.
Christchurch Hospital has said it might have to postpone treatment for some patients, saying it would contact them directly.
That would likely be the case in some other hospitals, but Te Whatu Ora chief of people Andrew Slater said the agency would not know the full impact until after the strike had finished.
Health services would still be available for those who needed them, he said.
Senior doctors and junior doctors from the other main union would still be working, and would be providing essential "life preserving" services.
The doctors taking industrial action are members of the Resident Doctors' Association.
One of the junior doctors in Dunedin today. Photo: RNZ / Tess Brunton
Senior advocate Melissa Dobbyn said they worked across the country and in every speciality.
They range from those just out of medical school, to those about to become specialists.
Most were due for a pay rise of about 20 percent in their latest contract, but there were two major problems with what Te Whatu Ora was proposing.
About 300 doctors working in areas such as radiation/ oncology, psychiatry, public health and those entering GP training would miss out on pay rises.
The second area of contention was that doctors in another union had reached a deal, however, it was higher than what the junior doctors' union had been offered.
Junior doctors on the picket line in Dunedin. Photo: RNZ / Tess Brunton
This could result in colleagues working alongside the union's members being paid more for the same work.
"And our members are saying, this isn't right, this isn't fair."
Dobbyn was asked if any deal might have to wait until the Budget is announced later this month so that Te Whatu Ora had more funds to possibly allocate for wages.
"This is such a vital workforce that the money needs to be found and it has to be found sooner rather than later."
The workforce was short 500 resident doctors and 600 senior doctors so was already in a crisis.
While doctors were reluctant to take strike action, "this is the future we're planning for", she said.
Health New Zealand Te Whatu Ora chief clinical officer Richard Sullivan said the country's EDs remained open and patient safety and welfare was the top priority.
He encouraged those who were unwell to contact their GP or Healthline (0800 611 116) first if possible.
Sullivan refused to comment on the strategy behind the approach Te Whatu Ora of cutting the pay for some doctors while raising salaries for others.
The matter would probably need to be resolved by an independent facilitator, he said.
A second two-day strike is planned from 16 May, and the union would take a vote on further action, Dobbyn said.
Meanwhile, Health Minister Shane Reti has sent a message to striking junior doctors, saying the government valued them.
Dr Reti said he would urge both sides to enter a stage of facilitation in bargaining.
"So I'd say to junior doctors, let's have further discussions."
Reti said he had been reassured the public should continue to turn up to appointments and the emergency department if needed.
Doctors in Dunedin have a dog summing up their situation. Photo: RNZ / Tess Brunton
About 50 doctors were on the picket line just after 8.30am near Waikato Hospital in Hamilton and were attracting a great deal of support from passing motorists, an RNZ reporter said.
"Winter is coming, doctors are going", "New Zealand trained Australia pays" and "Government prescription? Pay cuts" were among the placards they were carrying.
One picketer told her there were 13 patients waiting to see one doctor in the ED on Monday night.
In Dunedin, doctors had brought their dogs along - complete with placards around their necks with signs supporting their cause, an RNZ reporter observing the picket said.
Photo: RNZ / Tess Brunton
Dunedin Hospital lost its right to train junior cancer doctors because it did not have senior doctors and one doctor on the picket line was concerned the programme for young doctors hoping to become oncologists would be affected further.
Another doctor was concerned about burnout because of the very long hours they were forced to work.
In Wellington the mood was cheerful as doctors believed strongly in what they were doing, an RNZ reporter at the scene said.
Those taking part were especially concerned about possible pay cuts for psychiatrists as well as the likelihood of New Zealand becoming even more of a training ground for the health sector in Australia, as more doctors left to earn better salaries across the Tasman.
Some of those on strike in Wellington. Photo: RNZ / Krystal Gibbens
About 50 people picketed outside the regional hospital on Tuesday morning. Among them was president of the Resident Doctors' Association James Anderson.
He said the offer Te Whatu Ora had put on the table was unfair and included a "pay cut" for some of the vulnerable specialities such as psychiatry registrars, public health registrars and the future GP workforce.
Sarah Hanson, who is a psychiatry registrar, was among those affected.
She said the country was already short on psychiatrists, and if people were not paid fairly, some might not be able to continue their training.
Meanwhile, Dr Rosa Tobin Stickings told First Up the current pay offer was not good enough and they couldn't accept pay cuts for any union members.
Tobin-Stickings who is training to be an emergency registrar said with 500 resident doctors short across the country, shifts were getting "harder and harder".
It was not unusual to start work and be told she had to cover for another doctor.
"It's exhausting to be working in this environment and we've been working in this environment for some years ... and we're getting pretty burnt out."
Sometimes, the doctors had to apply for annual leave a year in advance and it was difficult to get leave for education puRposes or to attend conferences to help with their training.
Many junior doctors had enormous leave balances and so far Te Whatu Ora had not responded to how leave pressures could be improved, she said.