Some 40 local health staff employed by the Southern Health and Social Care Trust have been underpaid.
The total, which was revealed by the Department of Health, is the lowest for any of Northern Ireland’s health trusts, some of which incorrectly docked the pay of more than a thousand staff.
It follows ongoing problems dating back to last October with a new payroll system in health trusts.
The Department of Health said incorrect national insurance contributions had been deducted from some people’s pay, but steps had been taken to ensure it did not happen again.
Health Minister Edwin Poots has come under fire for failing to tackle the severe problem with the administration of staff salaries.
Unison says frontline staff have been pushed to the limit by a “totally shambolic” system.
A Department of Health spokeswoman said the minister expected all relevant organisations “to act quickly to redress any loss by staff”.
According to the department, the trusts have already implemented a range of measures to correct any errors – this includes running additional payment cycles to make good any underpayments and emergency payments.