In the meantime, staff have been receiving the last payment made before the system crashed because payroll cannot record or work out what hours people have worked and therefore what they are owed.
A nurse told the Herald this was problematic because they are a lot of shift workers at the hospital and their pay changes every time depending on hours or days worked. There could also be extra payments owed for missed breaks.
"Staff are likely either being underpaid or overpaid as a result and as the same payment is being repeated multiple times this effect will be compounded," the nurse said.
Staff were also not getting payslips at this time which meant they had no ability to even check they had been paid correctly.
Nurses Society of New Zealand director David Wills said he was also aware that some members who had received final pays had encountered some issues as the DHB was unable to accurately calculate the final amount owed because it did not have access to the records.
"People are accepting that as being unavoidable, but it's obviously causing them inconvenience."
A Waikato DHB spokesperson said it was working to correct staff pay as quickly as possible and this was being treated as a priority.
There was a significant amount of manual entry which must be completed to "catch up" both the roster and payroll systems to ensure staff are paid any and all entitlements earned during the outage before they could return to their normal pay runs, he said.
Any staff who believed they had been overpaid had been told to consider putting the additional amount aside so they would be prepared to return overpayments without experiencing a negative impact.
Association of Salaried Medical Specialists executive director Sarah Dalton said she had met with the DHB's executive team last week and was aware a number of staff were being underpaid.
"Clearly there's a massive chunk to do around payroll as well ... It is going to take them a while and it is going to be messy I think."
She said the DHB was doing the best they could given the circumstances and did have welfare measures in place to prevent hardship.
Speaking after the first payroll disaster when some staff weren't paid at all and emergency Prezzy Cards had to be issued to some, Waikato DHB chief executive Kevin Snee said he expected the following fortnightly pay run to be smoother and that they had better processes in place.