Corangamite Shire was singled out this week as one of four councils that had overcharged ratepayers - even if it was by pocket change.
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The average ratepayer was overcharged by 21 cents in 2018-19 - but the exact amount would be higher or lower depending on their property valuation.
The council has taken action to reverse the discrepancy with Corangamite ratepayers being undercharged an average of 30 cents this year.
The Essential Services Commission's Marcus Crudden said it was pleasing that the councils had taken action this year to ensure ratepayers weren't disadvantage.
Corangamite Shire blamed the incorrect rate notice amounts on property valuations amendments being received after the budgeted rate in the dollar was set.
The commission's audit this week found that for the first time in three years all 79 Victorian councils had complied with either the rate capping set by the state government or the higher amount approved by the commission.
Warrnambool City Council was one of four councils given the OK to lift rates by and extra two per cent over the State Government imposed 2.5 per cent cap.
Mansfield council lifted rates by 13.94 per cent, Towong council by 5.55 per cent and West Wimmera by 3.50 per cent.
The commissions report said that while it ran a range of checks on the data submitted by councils to validate their compliance, it does not independently verify the underlying data submitted by each council.
"However, each council's submission is certified as accurate by the council's chief executive officer," it says.
Mr Crudden said having 100 per cent compliance across the board was a good outcome for Victorian ratepayers.
"Councils have improved their processes for ensuring their average rate does not exceed the cap," he said.
"They are being more proactive about checking their rates early in the year, rather than waiting for our assessment, which has minimised costs to ratepayers," he said.
The rate cap for 2020-21 is expected to be announced by the state government next month.
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