Unions have warned strike action could take place if a glitch to a multi-million pound payroll system which has left thousands of staff underpaid is not fixed urgently.
Health Minister Edwin Poots has come under fire for failing to tackle the severe problem with the administration of staff salaries, which has been ongoing for months.
Unison says frontline staff have been pushed to the limit by a "totally shambolic" system that began last October.
A Department of Health spokeswoman said the minister expected all relevant organisations "to act quickly to redress any loss by staff".
But unions said they were prepared to ballot for industrial action. It is understood the problems occurred due to the health service's Payroll Shared Service Centre (PSSC) not receiving claims for overtime, travel claims and allowances, affecting thousands of staff.
The South Eastern Trust said that through additional payroll runs it had paid out £189,000, that affected 1,200 staff.
In addition the trust has also processed approximately 400 emergency payments totalling £274,000 from January to April.
An additional payroll run is planned for later this week.
The Northern Trust was unable to provide any figures.
The Western Health and Social Care Trust confirmed it was aware of 26 staff who had not received full payments in their April 2014 salary.
In April, 118 staff in the Southern Trust did not receive payment because of an "error" in processing payments.
The Belfast Trust said that between October and March 2014, it had made 3,002 corrections through additional payroll runs.
Unison's Ray Rafferty has called for an urgent meeting with the Health Minister to address the situation.
"I spoke to one nurse who, after all her direct debits and standing orders, had just £7.23p left in her account – she was owed more than £700," he said.
"We need people paid within the next 48 hours.
"If not, then we will put it to our members: are they prepared to take industrial action over this?"
A DHSSPS spokeswoman said the Mr Poots was "extremely concerned" that some staff had not received correct pay.
"Additional expertise has been provided to trusts to help them to minimise any future difficulties," the spokeswoman added.
STORY SO FAR
Thousands of hospital workers across all the Northern Ireland Health trusts have been affected by underpayment. It started last October following the implementation of the new payroll system. The trusts have apologised to workers and said measures have been put in place to address the problems. But unions remain angry at the ongoing problems.