Serious errors were made in the running of trains in Kent, the rail operator stripped of the Southeastern franchise has admitted.

The franchise was taken over by the Department for Transport (DfT) in October after the Go-Ahead Group failed to declare more than £25 million of taxpayer funding.

Go-Ahead says it expects to face a fine over the accounting error, although it said the full amount is unclear at this time.

Go-Ahead said: "Notwithstanding the complexity of the franchise agreements relating to LSER (London & South Eastern Railway Ltd), the review has found that serious errors were made by LSER with respect to its engagement with the DfT over several years.

"In particular, the group accepts that, by failing to notify the DfT of certain overpayments or monies due to the DfT, LSER breached contractual obligations of good faith contained in the franchise agreements. Accordingly, the group has apologised to the DfT.

"The behaviours identified by the independent committee which contributed to the management of LSER’s contract with the DfT do not reflect the values and standards of conduct that the group expects of its colleagues."

Go-Ahead said it believes it has a good corporate governance structure in place but that it will look at ways to improve it.

The company added that, as a result of the investigation, it will be delaying publication of its results until next year.

The Southeastern franchise had been owned by Govia – a joint venture between Go-Ahead Group (65%) and Keolis (35%) – since 2006.

Go-Ahead Group’s chief financial officer, Elodie Brian, resigned after the decision to remove the franchise was announced.