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The council announced on Monday the new fees for on-street parking - including increases of up to 50% in some areas - would be introduced beginning on Thursday.
The changes had been signed off earlier in the year and had been due to come into force on July 1, but were delayed by the need to update parking meter software.
However, one motorist contacted the Otago Daily Times yesterday to say parking meters in Water St were malfunctioning, advertising a rate of $1 per hour but charging $3 an hour.
"So when I put in my $2 expecting to get to 11am, I got to 9.40am.
"I wasn't happy."
She blamed the fault on a glitch in the meter's software, but avoided a ticket after leaving a note on her car's dashboard.
Council transport group manager Richard Saunders confirmed the Water St parking meters had been charging an incorrect rate following price changes earlier in the week.
"We're sorry for the error and are correcting this [yesterday]. Anyone who has paid at the incorrect rate can contact us for a refund using their parking receipt or ticket."
The council was aware of seven meters which had been incorrectly programmed - four in Water St, two in Cumberland St and one in Dowling St - but anyone with concerns about other meters was invited to contact the council.
The changes announced on Monday included lifting the cost of parking along George St - where a 30-minute maximum stay applies - from $1.50 to $2.
Four-hour parks in the outer zone will increase from $1 an hour to $1.50 an hour, while all-day parks in the outer zone, which used to cost $5 a day, will now cost $6.