The chief executive of the Association of Train Operating Companies has defended fare increases which average 6.2% and in some cases are much higher.
Michael Roberts said the rises were part of a government policy to make rail passengers pay a greater share of the cost than taxpayers.
The hikes will also result in "more trains and better services", he said.
But Anthony Smith, chief executive of customer watchdog Passenger Focus, said many passengers would be "baffled".
Regulated fares, which include season tickets, have gone up by an average of 5.8%, but some mainline season tickets have increased by almost 13%.
Some unregulated fares, typically short distance off-peak ones, have also risen by more than the 6.2% average but the industry has not given a figure.
Tube and bus fares in London have risen by an average of 6.8%.
Speaking to BBC - Radio 5 live's Weekend Breakfast, Mr Roberts said the above-inflation fare rises were the result of a broader policy decided by the government, rather than train companies.
"At the moment, (the cost of travel) is paid for half-and-half between the taxpayer and passenger. The government policy is that the taxpayer ought to pay a smaller share of that in the future, which is why fares are going up.
"The money raised will pay for more trains to address overcrowding, better stations and quicker journeys," he said.
He admitted that "in the current economic climate, any talk of increase is clearly something people are not going to be particularly pleased with" but said rail journeys were at an "all time high since 1940s - which is a sign people are able to buy the right ticket for the right journey".
The government and London Mayor Boris Johnson say the increases are necessary to support vital transport projects.
But shadow transport minister Maria Eagle said the changes were unfair and would be a "nasty New Year shock" for commuters.
"The government have given the train operating companies freedom to fiddle the fare rises by reintroducing something which the Labour government put a stop to - flexibility.
"Which means that they can charge commuters who have to get on particular trains even higher than the already high average while charging less on little-used routes," she said.
Anthony Smith, chief executive of rail customer watchdog Passenger Focus, said: "Many passengers returning to work in the new year will be baffled about why they are paying much higher figures than the 'averages' published by the train companies.
"With the train companies again free to raise fares on individual routes, some passengers will be facing rises way above inflation and in some cases it will be back to the bad old days of double-digit fare increases."
The Campaign for Better Transport said the cost of some annual season tickets exceeded £5,000 for the first time and warned the rises would price people off trains.
It says an annual season ticket for commuters travelling on services between London and Tonbridge, in Kent, has risen by 12.7% to £5,192.
A season ticket on the First Capital Connect stopping service between Peterborough and London, which was £5,000, is now £5,320.
Regulated fares are tied to an annual price cap formula meaning fares can increase each January only by the previous July's RPI inflation rate plus 1%. This means a 5.8% average rise for 2011.
However, companies are able to put up some fares by more than 5% as long as other fares decrease at the same rate. There is no price cap on unregulated fares.
In January 2012, passengers will have to dig even deeper into their pockets when the annual price rise formula changes to RPI plus 3% across the network.
The increase on my season ticket in monetary terms is modest, unlike my girlfriend's which is quite significant, however, I refuse to be held to ransom by train companies every year. What with the increase in petrol costs I've also disregarded driving to work - therefore I will cycle to work as I'm fortunate enough for this to be a viable option for me. I note the standard response from rail operators is that 'the fare rises are due to cuts in taxpayer funding', however, I was of the understanding that the proceeds from 'green taxes' that have been introduced would be invested in public transport improvements - so what is this tax revenue being spent on if the government is reducing rail funding? Ian Chappell, Wokingham, Berks
I'll keep on paying as I have no choice. This idea that people are able to find the right fare at the right price is complete nonsense. People will pay almost anything that the train companies demand as they have little or no other choice but to do so. Patrick, Stains
I understand the train companies argument that the train passengers need to share a higher proportion of running costs than the tax payer but we are now in a position where the railways are unaffordable for most people. My 40 minute train journey has increased from £2500 three years ago to £3400 today. The service is no better, the trains are no less overcrowded and Southeastern's communication when there is a problem borders on comical! If something is not done soon I and many others will simply not be able to afford to use the trains anymore. Add to this the fact that to park at the station now costs £1000 a year! It makes you wonder what the point of going to work is when you spend such a huge proportion of your salary just getting to work. It makes me furious. J Foster, Kent
I commute from just outside of Cardiff to just outside of Bristol. I believe that commuters might accept such fare increases if they could see the train operating companies striving to improve the service. Instead our trains have lost carriages, added not long ago to counter overcrowding, and there is a complete lack of interest in coordinating trains from different companies at Cardiff and Bristol. The fact is the whole franchise system is set up as a contract between state and rail companies, based on terms of carriage that date back to nationalisation. The priorities of the passengers are ignored and until train companies and Network Rail lose the whole fare for every inconvenienced passenger there is too little incentive for them to change. Jeremy, Cardiff
I drive to work and get NO subsidies on diesel or parking. Why should I subsidise other people going to work? GC, Fareham
My son travels to work in St Albans (two stops away from Borehamwood) and his fare today has risen by £2 off peak, and £3 during peak times. As he is on the minimum national wage, this now means that it will take him half of his day to earn back his fare, and the situation has prompted him to hand in his notice as he no longer feels it is worth his while to make the effort to work. I myself travel in the opposite direction into London and used to leave my car at home and take the train, but because of the increase I will now be forced to take my car each day as it will be much more economical even with the fuel rise, and I believe many people will be doing the same, which once again will greatly increase the amount of cars on the road. Stephanie, Borehamwood
This latest increase is just going to punish people like me even further. All many of us are doing is trying to use the trains to get to work just to earn an honest living. We were all ready paying, in my opinion, really extortionate fares for a very poor service. At they end of the day this should be a public service and be supported as such. I wonder how this fares increase sits with the government's efforts to reduce Co2 emissions. More and more people will just switch to using their cars instead and bring our already congested roads to a standstill. How very short-sighted! Peter, Colchester
It's just incredible how they see they need to rise ticket fares. Recently been in Germany to add to a number of european destinations where train travel is much cheaper than in the UK. Anthony, Worthing
I am not a regular commuter but I am a tax payer. If the government wants to reduce the burden on the tax payer for the railways and move it on to the fare payer can we assume that they are going to reduce income tax, if they don't they are just adding additional tax to the large number of tax payers who commute by train, and who usually have to travel at peak times. William Usher, Dalry, Ayrshire
I am not surprised that you have been given no figures for the rise in off-peak fares. The price of a ticket to Ipswich to go to football has risen 18.6% from £8.60 to £10.20. My trips to Carrow Road on the alternative Saturdays have risen by 13.6%. These trips are to carry out voluntary work with St John Ambulance. I can reclaim expenses but as my division only gets paid £26 for my attendance at football matches so it will soon not be economically viable to attend. The excuse that the fares are rising to alleviate overcrowding is false as the trains that I use are mainly over 50% empty. I am now looking to car share with some football supporters to save money. Mark, Diss
I find Mr Robert's statements appalling. The cost of my season ticket goes up and up - yet the quality of service goes down and down. The journey times now are longer than 5, 10, even 20 years ago and the carriages at rush hour are jammed to such a level that cattle have more space. And even when paying for first class, there is so little enforcement that second class ticket holders, desperate for a seat just take an empty first class seat. Rail travel, particularly to London, is a public service and should be run as such. The government should take a close look at how public transport works in places like, well, most of Europe! Thomas, Cookham