Flintshire council has overpaid a total of £330,000 to some of its staff and it is now asking for the money back.
Some employees have successfully argued they should not have to pay back the cash, says public sector union, Unison.
The council's head of human resources described the situation as unfortunate and said the problem was being dealt with "sensitively".
The mistake came to light as the authority made changes to its payroll system.
An internal audit found the overpayments go back to 2007 when £54,771 was overpaid to staff. That figure includes national insurance and pensions contributions.
Overpayments were also made due to problems with timesheets and changes in the number of hours worked.
The situation continued over four years with £155,100 overpaid in 2010.
Helen Stappleton, head of human resources, said: "We have been undertaking a programme of work over the last few months to improve and audit our human resources and payroll system and the data we hold on the system.
"Unfortunately, this work has resulted in the identification of some overpayments and underpayments of salary, all of which are being rectified speedily, sensitively and in accordance with our procedures.
"As part of this audit work, we have introduced improvements to our procedures and controls which will reduce the number of errors occurring in the medium to long term".
On Tuesday, Flintshire council's audit committee is due to receive an updated report.
It says: "Following discovery of the problem we have been advised that a review was undertaken of every employee's pension contributions and national insurance deductions."
The report says payroll payments to employees totalled £9.1m during March alone. The money was paid to a total of 7,991 employees, although workforce information reports indicate there are 9,176 people on the payroll.
The report does not say how many individuals have been overpaid or how much they received individually.
But Unison branch secretary Sarah Taylor said she was aware of some individual cases amounting to more than £5,000.
She said the union had represented a number of staff, some of whom had won their argument that they should not have to pay the money back.
She said those cases had been won on the grounds they did not knowingly receive overpayments, that the money had been spent and would cause hardship to repay.
Connah's Quay councillor Bernie Attridge first looked into the situation when his wife, Leanne, a school taxi escort for the council, was told she had been overpaid by £600.
"A lot of work needs to be done on this to make sure it does not happen again," he said.