Hundreds of builders have been overcharged for their licences over close to two decades.
The South Australian Government said the Office of Consumer and Business Services found it had been routinely making mistakes since 1996.
The Government has apologised for the costly mistake and promised to give refunds to those builders who have been overcharged.
But it is still working out how many builders might owe the government money if they were charged too little.
An independent audit has found hundreds of cases of builders being overcharged, some for an extended period.
Deputy Premier John Rau said they could now expect refund cheques.
"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.
There is less certainty about what may happen to builders who have been undercharged for licences.
"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.
"[It seems to have been an] administrative or clerical error. Whatever the nuts and bolts of that are, it's a mistake, it shouldn't have happened."
The mistake could leave taxpayers as much as $400,000 poorer.