The South Australian Government says the Office of Consumer and Business Services found it has been overcharging builders for their licenses for nearly two decades.

The Government has apologised and promised to give refunds to builders, who have been getting short-changed since 1996.

Reports say it is unclear whether some builders may have suffered in the opposite way, being undercharged for licenses and now left owing.

The revelations came from an independent audit, which turned up hundreds of cases. Refund cheques are already on their way, according to SA Deputy Premier John Rau.

“In most cases that amounts to a few hundreds of dollars but in one case I believe it might be as much as $6,000,” he said.

As for the builders who have been undercharged: “We're looking into that aspect as well but, look to be perfectly frank, if we have an undercharge that dates back to 1996 I think we're going to have to take that on the chin,” Mr Rau said.

Some estimates say the ongoing mistake will now cost taxpayers up to $400,000 to rectify.

“Whatever the nuts and bolts of that are, it's a mistake, it shouldn't have happened,” the Deputy Premier said.