Staff at Wellington Regional Council have been over-paid and under-taxed for almost a decade.
The mistake could mean it owes millions to Inland Revenue.
It realised the error when changing the payroll system, and found it had been miscalculating tax deductions for employer KiwiSaver contributions for nine years.
The Wellington Regional Council said the mistake occurred when the Employer Superannuation Contribution Tax system was introduced and set up in the pay system in 2012.