Some staff at United Bristol Healthcare Trust have been given cash advances to cover the shortfall, which has been a problem since the system was introduced last August.
Some have seen mistakes in their monthly salary, while others have not received payments for extra bank shifts or for anti-social hours.
The trust does not know how many of its 6,000 employees have been affected.
Staff have been told not to contact the trust’s payroll department by phone to report problems.
Instead, the organisation’s finance director Paul Mapson has sent them a letter telling them to use an electronic tracking system.
A spokesperson for the trust said the organisation hoped the pay issues would be remedied ‘comparatively quickly’.
‘UBHT values the hard work of its staff and is sorry there have been some recent difficulties providing a satisfactory payroll service,’ he added.
However, Unison deputy branch secretary at the trust Val Walker said the new pay system for staff had been ‘atrocious’.
‘We’ve seen cases where some people have been paid double and others not at all – some staff have had to take out loans to cover their mortgage payments because they haven’t been paid,’ she said.
‘We are waiting to see whether the problems are eased. We still have several grievances outstanding because, ultimately, not paying people is breaking the law,’ she added.
A Department of Health spokesperson said officials were ‘extremely concerned about the problems United Bristol Healthcare Trust is experiencing in providing payroll services using the NHS Electronic Staff Record’.
‘We are working closely with colleagues at [the trust] to identify the problems and to provide support in achieving a timely resolution,’ she said.