The report concluded that the GTR franchise has not yet given value for money, although it does have a ‘realisticˆ chance of doing so eventually. The Department for Transport was one of the NAO’s targets, partly because it did not make sure when the franchise began that it had enough drivers.

Apart from the staff shortage, the development of the Thameslink Programme has also been hampered by infrastructure failings as well as chronic industrial action.

When RMT members on Southern staged another strike on Monday, it was the 39th stoppage in the dispute over driver-controlled operation. Strikes over DCO and DOO have been continuing on other operators this week as well, with further walkouts on Wednesday and today on Northern, Merseyrail, South Western Railway and Greater Anglia. The effect of the strikes has varied, with noticeable disruption on Merseyside and Northern, less so on Southern and a full service reported by Greater Anglia.

The RMT said support for its action remained ‘rock solid’.

Meanwhile the Mayor has seized upon the Thameslink problems to renew his call for more TfL control.

He said: “This is yet more damning evidence of the terrible services inflicted on London’s rail passengers by Govia Thameslink and the Government. It’s no wonder Londoners are so fed up with services that are regularly late, overcrowded and increasingly expensive. It’s vital that the Government leaves behind its broken franchise model and devolves more commuter routes to TfL. Only then can Londoners finally get the affordable, high-volume, high-frequency suburban metro services they deserve.”

The DfT said: “Clearly the disruption passengers have experienced is unacceptable but the NAO recognises that service has improved over the last 12 months. The government has taken a number of steps to ensure this improvement, including the provision of an additional £300 million to improve reliability on the Brighton Main Line.”

RMT general secretary Mick Cash said: ““This dynamite report blows wide open the whole scandal of the Thameslink, Southern and Great Northern franchise and the scale of Government collusion with the private train operators, which has bled the taxpayer dry while giving this basket-case operation a free hand to slash staff and run services into the ground.

“The report makes it clear that tens of millions of pounds of public money, cash which could have guaranteed a guard on the trains and delivered decent, accessible rail services, was instead wasted propping up the private owners while they presided over the worst rail franchise in the country. This is a scandal of epic proportions with Chris Grayling and the Tories centre stage and worst still they are about to embark on an even bigger taxpayer bail-out on the privatised East Coast Main Line.”