The apology came after Strath Taieri Irrigation Group secretary Kate Wilson spoke at the council's public forum yesterday, saying the low-flow monitoring charge came as a shock to users and was "unfair and inconsistent with the council's stated aims".
"To continue in its current form will only lead to frustration between farmers and council when there has been considerable goodwill on the part of farmers to resolve the issues."
Council chief executive Graeme Martin said the error in calculating the council's new annual water user charges was discovered when it reviewed its charges for checking compliance with conditions on resource consents.
The error involved about 100 rural water users who had been "erroneously invoiced a $715 fee" for water low-flow monitoring, he said.
"An error has been made and I apologise to ratepayers and councillors. The error will be corrected immediately."
Where the invoice had been paid, the money would be reimbursed, he said. Where the invoice had not yet been paid, a credit note would be issued.
The error arose from the way in which a team of staff established the new charging system, Mr Martin said.
The team applied one element of the charge rules without applying an override provision.
Some council resource consents had charges for monitoring sites established by the council specifically to monitor and control conflicting water takes.
It was only these later consents that were subject to the water low-flow monitoring charge, he said.
Last year, the council resolved the cost of consent monitoring services would be funded 50% by the consent holder and 50% from general rates.
Previously, this was funded entirely from general rates.
This was publicly notified through the 2008-09 annual plan consultation process and by letter to the affected consent holders.