Thousands of Victorian ambulance service staff were paid the incorrect amount of superannuation for more than six years.

Three days after Ambulance Victoria's CEO resigned amidst a protracted pay dispute, an external review has revealed about 3000 employees were affected by payment errors between July 2017 and December 2023.

Some superannuation guarantee contributions were underpaid while others were overpaid due to wage code errors.

"Please be aware that this error is in no way the fault of the workers in the AV payroll department," a Victorian Ambulance Union said in a bulletin

"Once again this highlights the need for AV to invest in proper payroll systems, readable payslips, and enough payroll staff to handle the growing workload."

Underpayments were below $1000 for most employees.

The money owed, plus 10 per cent interest a year, has been sent to the tax office and will be passed on to staff's nominated superannuation accounts, Ambulance Victoria said in a statement.

"We want to apologise to those who have been impacted by this wage code error and we have started the process to repay staff members whose superannuation has been underpaid," an AV spokeswoman said.

"This impacts employees who are members of accumulation superannuation funds, which is primarily our corporate and casual/surge workforce."

The service said the error had been resolved and that it won't seek to recover overpayments.

The mistake comes at a tumultuous time for the service, after Jane Miller resigned as chief executive on Tuesday.

Her resignation after 18 months in the role came after the ambulance union passed a vote of no confidence in the service's leadership.

In July, six members of its payroll department were stood down over an alleged $3.5 million embezzlement scam and subsequent accusations senior management leaked information about the investigation.