The former operator of the Southeastern rail franchise, Govia, has been fined £23.5m over financial irregularities.
The Department for Transport (DfT) announced the penalty after the group failed to return more than £25m in taxpayer funding.
A spokesman for the train operator said they had "accepted" the penalty.
Govia was stripped of the Southeastern services last year, following a review by the DfT.
In addition to the penalty, the government is recovering £64m from the rail company's operator, London and South Eastern Railway Limited (LSER), that is owed over the scandal.
Transport Secretary Grant Shapps said the company had been found to have committed an "appalling breach of trust".
Mr Shapps said: "LSER's behaviour was simply unacceptable and this penalty sends a clear message that the government, and taxpayers, will not stand for it."
A government review also found that the train operator had concealed funding during its previous franchise agreement that ran from 2006 until 2014.
A spokesman for the train operator said: "We accept this penalty. Since these events came to light, our corporate governance procedures have been enhanced and the group is under new leadership."
Despite losing the Southeastern franchise, Govia continues to operate Govia Thameslink Railway.