The resignation of Stephen Byers once again throws the future of the government's transport plans into confusion.

Professor David Begg, chairman of the Commission for Integrated Transport, said: "We can't keep changing transport secretaries at the rate we do and blame each one for the mistakes of successive governments. Whoever the new transport secretary is has to accept that improving our transport network will be a long haul."

Charles Secrett, director of Friends of the Earth, said that Byers' departure "will not take one car off the road". He added: "It will not sort out the crisis on our railways. It will not create a decent transport policy from the under-funded shambles that is the 10-year transport plan."

A spokesman for Railfuture, the independent campaign for rail users, said: "It has been obvious that Stephen Byers has recently not been in control of transport and it was only a question of time before he was either replaced or had to resign."

Mick Rix, general secretary of Aslef, the train drivers union, said: "This is a sad day for the railway industry. I hope that the government's policy of starting to re-establish public control over the industry will continue under Stephen Byers' successor."

Sir Richard Branson, the boss of Virgin trains, said Byers had achieved much but had to go. "Since his assistant made a very foolish statement it's been difficult for him to concentrate on the job," he said.

Anthony Smith of the Rail Passengers Council said "that last thing the industry needs at the moment is more uncertainty".