From 5 January, some tickets will rise by more than twice the rate of inflation.
TICKET PRICE CHANGES
The fare hikes have been criticised by passenger groups, who questioned why price rises were necessary when performance often remained so poor.
Some fares on Connex South Eastern, recently given a £58m government hand-out, are to rise by 7%.
Leisure tickets on the Virgin Cross Country network, which stretches from Penzance to Aberdeen, are going up by 5%.
But season ticket holders on nearly all lines will get discounts of up to 10% next year, as compensation for poor service this year.
The average price rise will be 2.5% - just under the rate of inflation.
"
Passengers will find it difficult to see how companies who regularly have poor performance records, are
now entitled to put up prices
"
Rail Passengers Council
Regulated fares - such as peak-time commuter and season tickets - are rising by an average of 2.4%.
Unregulated fares - such as walk-on long-distance travel - are rising an average of 2.8%.
Wessex Trains and Island Line have frozen their fares while Anglia Trains has cut its mainline season ticket fare by up to 4%.
But many fares for London-bound commuters are to rise by over 3%.
Recent figures showed that one in five trains were late during the summer.
"
It's been a tough year
"
George Muir, ATOC
George Muir, director general of the Association of Train Operating Companies (ATOC) defended the price rises, saying they were coupled with "huge investment" on rolling stock which will benefit passengers in the future.
He told BBC Radio 4's Today programme: "It has been a tough year. I wish we could have offered a better service to passengers but track problems have been far worse than we expected."
He said after the Hatfield crash, the condition of the track and track bed was found to be "immensely worse" than expected, coupled with a 30% increase in traffic on the railways.
But Rail Passengers Council chairman Stewart Francis criticised the pay rises when performance on many routes remained "so poor".
"While we are pleased to see that operators have had the sense not to go for extravagant increases on unregulated fares, we are concerned by some increases of up to 3.5% on the walk-on fares which play an important part in attracting people on to the railways."
FARE RISES
The ATOC says many train operators actually reduced many fares last year, with investment and improvements continuing.
'Outdated' regime
The regulations currently allow a company that improves on its performance the previous year to raise fares - regardless of its overall level of service.
Mr Francis said: "Passengers will find it difficult to see how companies like Connex and South West Trains, who regularly have poor performance records, are now entitled to put up prices by an extra 2%.
"It is a confusing system which is well past its sell-by date."
This will be the last year for the present fares regime. A new system is expected to be in place in time for the annual fares change in January 2004.