Transport group Go-Ahead has been ordered to pay £51.3million to the government over its failures in running the Southeastern rail service.
The company, which was stripped of its licence last October, said the repercussions will cost it £81.3million in total.
The bus and rail operator lost its contract to operate the commuter network last autumn after the government uncovered discrepancies running over several years since 2014.
The transport secretary, Grant Shapps, said at the time that an investigation had found that since 2014, Southeastern had not declared more than £25million of historical taxpayer funding that should have been returned, and described this as a serious breach of the franchise agreement’s “good faith” obligation.
He said the money had been recovered and further investigations were being conducted into historical contract issues related to the franchise.
Chief executive Christian Schreyer apologised for the problems, as the company identified "serious errors" in the way the franchise was run and over the way it dealt with the Department for Transport.
That included failing to declare more than £25million of historic taxpayer funding which should have been returned.
New boss Christian Schreyer, who joined in November not long after the franchise was lost, said he was "optimistic" the issues over the franchise could be resolved soon.
He added: "It's been a very challenging year for Go-Ahead and our shareholders, for which I apologise, on behalf of the board."
The company has already apologised to the Government for the failings, which had led to the firm's shares being suspended from the London Stock Exchange as accountants needed more time to work out what impact the problems meant for the company.
Bosses also highlighted that a further £21.3million hit could be taken as part of the financial implications relating to the Southeastern franchise in relation to other negotiations with the Government.
A business review is now under way and is expected to report back in the next few weeks.
Elsewhere in the firm, which also runs regional buses, bosses said there had been a recovery in passenger numbers, although there was a temporary decline when the Omicron Covid variant emerged.
Regional bus volumes are currently at around 80% of pre-pandemic levels, it added.
