The parent company of Go Wellington bus services denies the amount of money pocketed by some of its drivers is as much as $500,000.
The Tramways Union says it was told by management that was the figure estimated to have gone missing over the past three years.
The union says the bus company did not have a proper electronic system to tally up how much individual drivers collected on their shifts.
However, it now does thanks to the introduction of a debit card and other system changes.
The Go Wellington service is owned by New Zealand Bus. Chief executive Bruce Emson says he will not speculate on how much money is missing, but it did not involve ratepayer funds.
Go Wellington receives $12.4 million annually from Wellington Regional Council.
The Tramways Union says nine fired drivers are being investigated by police over the theft of $20,000 in fares since May this year.
A driver employed by Go Wellington earns a salary of up to $41,000.
Mr Emson says the public can still have confidence in the bus system.