District health boards are challenging a union's democratic practices in their bid to prevent the next strike by resident doctors.

In the Employment Court at Wellington next Thursday, they will ask Judge Bruce Corkill to prevent the Resident Doctors Association's 48-hour strike, which is scheduled to start on the following Wednesday, November 23.

In explaining their bid for an urgent injunction against the strike, the DHBs claimed the union "included medical students in its most recent ballot to try and boost the low numbers that participated in the first strike".

They also say many new graduates starting as resident doctors will miss out on compulsory orientation with their DHB employers because of the strike, and the walk-out might leave some existing doctors having worked too few hours in their first year to move up to the next step in Medical Council registration.

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The DHBs' spokeswoman, Julie Patterson, said they were concerned the union had held just one strike ballot across all 20 DHBs.

"The circumstances of the RMOs (resident medical officers) within each DHB are different and they should have had the opportunity to conduct their own vote in relation to the strike action. Otherwise there is a risk that the tail could wag the dog.

The union said earlier this afternoon the DHBs claimed that because the unionised and recently graduated-doctors were not employees at the time they were balloted for strike action, they could not strike even though they would be employees when the strike occurs.

Union national secretary Deborah Powell said: "The decision of the DHBs to apply for an injunction is unfortunate. If successful, our strike will simply be delayed, not stopped, and is likely to push industrial action into the busy Christmas and New Year period."

"We had hoped we would have safer rosters agreed to before the graduating class of 2016 started working on the wards. We do not want yet another year of doctors to become worn out and worn down by fatigue.

"It would be nice to think the upcoming strike could be avoided, not by legal action, but by settlement of the contract. All we need is for the DHBs to return to the bargaining table to negotiate a fair deal."

Patterson, the Whanganui DHB chief executive, said the only outstanding issue is "that the DHBs are refusing to pay for the days off the RMOs will get on the [offered] new rosters".

She called for a vote on the DHBs' offer by all of the affected members in the union.

The strike starting on November 23 is scheduled to be a 48-hour walk-out, on the pattern of the union's strike in October. The last strike led to the postponement of thousands of elective surgeries and outpatient appointments as public hospitals focused on caring for acutely sick or injured people.

On Monday, the DHBs said they were surprised the union had rejected their latest offer, which included a 5 per cent pay rise over three years, and a payment of $200 when working a weekend shift.

DHBs' spokeswoman Julie Patterson said the offer gave the union "what they have been publicly asking for: a contractual guarantee that no RMO [resident medical officer] would work more than four nights or 10 days in a row".

The DHBs have said the union expected doctors to be paid for days off resulting from the roster changes.

The union said the DHBs' offer would on average cut members' pay by $5000 to $7000 - even with the $200 payments - because by working fewer hours they would drop into a lower salary band in the collective agreement.

"The DHBs have proposed a system that would see thousands of dollars being deducted from each RMO's salary, far out of proportion to the number or value of rostered days off they may get under safer hours rostering."

The union was also concerned that the DHBs had not contractually committed to the safer hours.