Some fares are rising 10% in the New Year
The rises emerged as Transport Secretary Stephen Byers admitted the UK's railways were worse than when Labour came to power in 1997.
Business passengers on some long-distance routes and buyers of walk-on fares will be the hardest hit by the rises.
The largest increase will be on Midland Mainline, which runs services between London, Leicester, Derby and Nottingham.
Its first class and standard open fares will be rising by 10%, dwarfing current inflation rates of less than 1%.
Great Western and GNER are also raising fares by about 4.5%, with Virgin the only cross-country operator to freeze fares.
Services 'worse'
But in the south-east of England, commuter lines are being forced to lower some ticket prices because of continued poor services.
Many season ticket prices will be up to 7% cheaper, making some fares lower than they were a decade ago.
Mr Byers said the only definite target the government was working towards was to increase passenger numbers by 50% over 10 years.
Speaking to BBC Two's Newsnight programme on Thursday evening, he said the follow-on from Railtrack being put into administration would be progress in punctuality, safety and comfort on the rails in time for the next general election.
Mr Byers said spin doctor Jo Moore, pilloried for an e-mail suggesting news be "buried" on 11 September, would continue to work for him and he would resist calls for his own resignation.
He said: "I will be here long enough to be able to discuss it with you at the next election and to outline the improvements we have been able to make as a result of the decision I took on 5 October to place Railtrack in administration.
Next election
"I want to see a railway system which is safe, which is punctual, with carriages that are clean and comfortable.
"In four or five years' time, when the next election is called, we can go through the situation as it is today and the improvements we will have seen by then."
Asked whether things were better on the railways now than when Labour came to power, Mr Byers said: "Of course they are not. They are worse."
But he put problems down to a "failed Tory privatisation", which was burning money while making matters worse.
He asked: "What could we do? We could muddle through, leave Railtrack there, part of the problem not part of the solution.
"Or we could say, 'Railtrack, no longer a blank cheque from the government. Let's put in place a new structure that will really make a difference'."