Southeastern railway services, one of Britain’s busiest commuter networks, has come back under direct public control, after the government stripped the private operator of its franchise agreement.

Ministers announced last month that an investigation had found that Southeastern had failed to declare more than GBP25m of taxpayer funding that should have been returned, describing this as a serious breach of the franchise agreement’s “good faith” obligation.

Train services on the line, which stretches across Kent and parts of East Sussex and connects them with London, will be run by the Department for Transport (DfT) from Sunday onwards under the Operator of Last Resort (OLR) scheme.

Passengers are not expected to see any immediate changes on the railway following the change of operator, with trains, timetables and fares staying the same, and staff remaining in place.

The Southeastern rail franchise was previously owned by Govia, a joint venture between Go-Ahead, with a 65% share, and France’s Keolis.

At its peak before the pandemic, Southeastern carried about 640,000 passengers a day on commuter routes, including fast services on the HS1 line.

Following the loss of Southeastern, Govia is left with Govia Thameslink Railway (GTR), which runs the Thameslink, Southern, Great Northern and Gatwick Express services.

Meanwhile, Go-Ahead also runs trains in Germany and Norway. It is the biggest operator of buses in London.

The chairs of Go-Ahead and Keolis said they would conduct an internal investigation following transport secretary Grant Shapps’ announcement last month.

Go-Ahead’s chief financial officer, Elodie Brian, resigned after the government decision was announced. She was previously the finance and contracts director of Southeastern.

Shapps said at the time there was “clear, compelling and serious evidence” that the franchise had committed a breach of trust, adding that the missing money had been recovered.

He said further investigations were being conducted into historical contract issues related to the franchise, while further options for enforcement options, including fines, were being considered.

Anthony Smith, chief executive of passenger watchdog Transport Focus, said: “Whoever runs Southeastern, passengers will want a reliable service which delivers on their key priorities: a punctual, reliable, clean train, with enough room to sit and stand, and value for money fares.”

Southeastern becomes the latest railway line to come under the OLR, which runs services previously privately operated by two other franchises.

The OLR launched the London North Eastern Railway (LNER) in June 2018, the London-Edinburgh-Inverness service, after operators Virgin and Stagecoach could no longer make the contract payments.

It subsequently introduced Northern Trains in March 2020, after the government renationalised the struggling Northern rail franchise, following years of widespread train cancellations and delays, when it ended the contract of Arriva, a subsidiary of Germany’s state-owned Deutsche Bahn.