Those using the Boundary St car park early in the day were charged $2 an hour instead of 50c, while those patronising the Ballarat St car park were charged the old fee of 50c an hour instead of $1.
The council's transport manager, Denis Mander, said he did not know how many people were affected.
"No-one came in and told us, but if someone has been overcharged they just need to bring their pay and display ticket in and we'll refund them," he said.
Earlier, in a press release, Mr Mander said it was "disappointing" the problem occurred on the first morning new parking charges were introduced.
The pay and display machines, provided by Global Integrated Solutions Limited, had "unfortunately displayed the wrong amount".
"It's disappointing, but fortunately we picked it up pretty fast thanks to some informed members of the community and an early morning call to the council."
