The Department for Transport found the group’s London & South Eastern Railway franchise (LSER) concealed excess funding for the High Speed 1 rail link from October 2014 to March 2020. Instead of returning it to the Government, LSER kept the money.

In September, the DfT nationalised LSER’s franchise and recovered £64million it said it was owed for breaching its franchise agreement, profit-share pay and interest due.

The department said it also identified evidence of similar behaviour by LSER during its previous franchise agreement, which ran from April 2006 to October 2014.

Transport Secretary Grant Shapps described the company’s behaviour as an “appalling breach of trust”.

He said: “LSER’s behaviour was simply unacceptable and this penalty sends a clear message that the Government, and taxpayers, will not stand for it.”

Clare Hollingworth, Go-Ahead’s chairman, apologised for the LSER scandal in September.

The transport group, which had set aside £30million to cover fines relating to the rip-off, employs 27,000 in its bus and rail businesses in the UK, Singapore, Ireland, Norway and Germany.

Go-Ahead and Keolis of France have 65/35 ownership of LSER.

Go-Ahead’s Govia Thameslink Railways business operates the Southern, Gatwick Express, Great Northern and Thameslink rail franchises.

Meanwhile, National Express has urged Stagecoach shareholders to back its revised takeover bid for the bus operator, rather than the £549.9million or 105p-a-share deal the board agreed with German investment group DWS.

Southeastern train National Express initially offered an all-share deal that valued Stagecoach at 87.8p, but returned yesterday with a new offer valuing it at 170p a share.