Go-Ahead Group PLC (LSE:GOG) was fined £23.5mln by the UK government for an "appalling breach of trust" at its London & South Eastern Railway (LSER) franchise.
The Department for Transport (DfT) also ordered the public transport company to repay £64mln to taxpayers after it identified what is described as fraudulent activity dating back to 2006.
Go-Ahead previously said it paid the government £49.2mln and anticipated a total cost of £51.3mln.
The £23.5mln financial penalty was £6.5mln lower than the £30mln provision the company had made in its final results.
Overall, the cash cost is around £15mln less than the company has been holding in restricted cash, said analysts at broker Peel Hunt, meaning "more cash can be distributed to LSER's owner, Govia", of which Go-Ahead is a 65% shareholder, with the rest owned by Paris-based Keolis.
Go-Ahead and Keolis deliberately concealed over £25mln in historic taxpayer funding for the UK’s first section of high-speed rail, known as HS1, between 2014 and 2020, which should have been returned to the taxpayer, the government said.
There is also evidence that LSER engaged in similar behaviour during its previous franchise agreement, which ran from April 2006 to October 2014, a statement added.
Shares in Go-Ahead leapt over 15% to 715.24p on Thursday morning.
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