Wellington health workers, including doctors and nurses, have been missing out on allowances, overtime and holiday pay because of a payroll system described as "diabolical".

"If we made those kind of mistakes in our roles that payroll are making, patients would die," one unnamed nurse at Capital & Coast District Health Board said.

"I think the feeling amongst members is that Capital & Coast doesn't care enough to get the pay right," Deborah Powell, an advocate for more than 500 medical and health practitioners at CCDHB, said.

KENT BLECHYNDEN/ FAIRFAX NZ Wellington Hospital, where some of the Capital & Coast DHB staff have become frustrated with continuing payroll problems.

Powell, from the Association of Professional and Executive Employees (Apex), said payroll problems affected all DHBs, but Capital & Coast's had been a "nightmare".

Despite some improvements, it was "among the bottom third" of all DHBs in terms of "sheer quantity" of payroll problems, eclipsed only by the massive conglomeration of Auckland and Northland's four DHBs, she said.

"They're always in catch-up mode. They're just constantly chasing their tail."

The health board has suffered payroll problems since as far back as 2012, when it reported 5757 total underpayment incidents.

Some staff have reported being overpaid, but most complaints relate to underpayment.

New Zealand Nurses Organisation organiser Georgia Choveaux said: "Because pay rates differ significantly between shifts and days, the nursing team often find it hard to even know whether there is a problem with their pay or not."

Ian Powell, executive director of the Association of Salaried Medical Specialists, said: "Generally it's unsatisfactory, and some would say diabolical."

There had been recent improvements, but "it's still very very slow and it really is unreliable in terms of people knowing whether they've been paid the right amount or not."

Deborah Powell said constantly checking for payroll mistakes was undermining staff morale and there was a "snowball effect" with routine pay issues absorbing the time of payroll staff, which often left one-off problems neglected.

"It's exhausting. To have to check your pay is another thing on top of what is a mentally and physically demanding job.

"Our members describe just being deflated and giving up. They work hard and expect pay should not be one of the hassles in their lives."

She said Apex intervened in December on behalf of more than 50 CCDHB radiographers on several issues while other staff waited for shift and on-call leave to be processed.

CCDHB's payroll was under-resourced and unnecessarily complex, but the payroll errors were probably not a deliberate or malicious strategy, she said. Nevertheless, there were too many errors and the response time in sorting out payroll mistakes was too slow.

One person familiar with the payroll system said it had been tweaked several times, comparing it with a house that had structural problems on which cosmetic work was done, but underlying issues never fixed.

CCDHB chief financial officer Tony Hickmott said the health board took issues affecting people's pay seriously. Every fortnight it processed pay for about 5100 workers, across 20 multi-employer collective agreements.

"A small percentage of people raise issues with us following pay runs. At the start of each year, issues can also occur when the DHB has large intakes of new staff including junior doctors and nursing graduates."

Pay issues generally arose around rostered workers, or new staff who worked different shifts and had some extra payment arrangements for overtime and shift allowances, he said.

"When issues are raised we prioritise them, and where necessary make a special payment to affected people, so that they do not have to wait until the next pay-cycle.

"We appreciate that any issue with a person's pay is frustrating, and we are constantly looking for ways to improve the many business processes that surround pay."

In 2012, timesheets submitted late were blamed for the highest number of underpayments, the DHB said in an Official Information Act response at the time.