Labour colleagues last night expressed regret at Stephen Byers' resignation as opponents asked why the decision to quit had not come sooner.
The Conservative party described him as a "dreadful minister" whose departure had been long overdue, and blamed Tony Blair for delaying the inevitable for so long.
"Stephen Byers has gone but the damage he has done to our roads and railways will last for years," a Tory party spokesman said. "We have been calling for his resignation for months. He has been a dreadful minister and he has gravely undermined this government's reputation for telling the truth.
"The prime minister must take the blame for clinging on to this discredited minister for so long. However, Mr Byers' overdue departure will do nothing for our crumbling transport system. The real scandal of the Byers era has been the total failure of the government to implement a sensible plan for improving our railways and easing congestion on our roads."
The Liberal Democrat leader, Charles Kennedy, said Mr Byers' position had become untenable and he had "finally done the honourable thing".
"While this is a personal tragedy for Stephen Byers, the most important thing is not the fate of an individual minister, but giving the British people a safe and reliable transport system fit for the 21st century," he added.
The party's transport spokesman, Don Foster, said: "Stephen Byers's departure was delayed even longer than the trains over which he presided. He has done the right thing in resigning, but it was a pity he only mentioned the needs of the government in his statement, not the needs of the travelling public."
The Scottish National party's leader at Westminster, Alex Salmond, said the resignation had destroyed the credibility of Mr Blair and New Labour, which he described as "one of the most deceitful political organisations in history".
"Tony Blair defended Byers at every turn, instead of sacking him long ago. And the culture of deceit and cronyism that Stephen Byers stands for runs right through New Labour," he said.
A solicitor who represents victims and families from some of Britain's worst rail disasters said the resignation was only the first step on the road to restoring public confidence.
"The problem for the victims of rail crashes, including Potters Bar, is the government transport policy, rather than the identity of the secretary of state," said Louise Christian. "There is not enough investment and long-term planning."
But the Association of Train Operating Companies expressed regret about Mr Byers' departure. Its director general, George Muir, said he had always found Mr Byers "thoughtful and open".
There were also kind words from Digby Jones, director general of the Confederation of British Industry. "I never questioned his genuine desire to address the deep-seated and long-standing problems facing the transport sector," Mr Jones said. "The government must remain fully committed to driving through the 10-year transport plan. It is a vital framework for delivering the improvements our economy desperately needs."
Those who worked closely with Mr Byers expressed sympathy and regret for a man they described as honourable, dedicated and brave.
David Triesman, general secretary of the Labour party said: "In each ministerial post, serious progress was made, and at transport, after years of neglect and botched Tory privatisation, Stephen had started the process of renewed rail investment based on sustainable plans. These involved tough decisions and it is a sad reflection that the Tories who had left such an appalling legacy were unscrupulous in attacking him."
The Northern Ireland secretary, John Reid, said: "He has been a staunch colleague who never shirked difficult decisions. He acted honourably and I fully appreciate the reasons why he decided to resign."
The Labour MP Glenda Jackson, a former London transport minister, said it was a shame that the "extremely capable and very dedicated and energetic" minister had been "hounded out of office".
