The Rail Delivery Group - responsible for policy formulation for the rail industry - says although some ticket prices will rise on average by 3.1 percent, the overall figure is 2.8 per cent.
The 3.1 per cent figure takes into account fares described as "regulated" - these are annual season tickets and inter-city tickets.
However, taking into account "unregulated" fares - tickets with prices set by train operating companies, including first class and advance purchase fares - the overall rise would be 2.8 per cent.
“We strongly support the Government’s decision to limit the average increase in Season ticket prices this year. This, combined with the determination of train companies to continue attracting passengers, means the average increase across all fares is 2.8%, the lowest in four years. To help the Government hold down fares in future, the rail industry is working hard to get more for every pound it spends.
“This year and in coming years, passengers across the country will continue to benefit from billions of pounds spent on improving services. As well as introducing more carriages, work will proceed on major projects like the new Birmingham New Street station and thousands of smaller, less visible schemes to improve the railway.”
Train companies retain an average of just 3p from every pound paid for rail tickets, with the vast majority of revenue going on maintenance, staff costs and investment in the rail network, according to figures released by the industry association the Rail Delivery Group:
Rail fares increase from today - with annual tickets rising by an average of 3.1 per cent.
A campaign group has claimed the latest rail fare price rise will mean increasing financial worries for commuters.
The increase means an annual 12-month season ticket for Leeds to Wakefield will rise from £964 to £992 - a 2.9% increase.
The belief the Government sees the railways as a "cash cow" was "just a nonsense", according to a transport minister.
In an interview with Daybreak, Stephen Hammond defended rail operators in the face of fare rises, claiming companies like First Great Western and Southern Railway only make "three pence in every pound".
He also claimed "much of the fares passengers pay" go directly back into the railways and are being used to fund projects to tackle overcrowding.
The shadow transport secretary has refused to rule out renationalising Britain's railways in a bid to lower ticket fares and provide a better service.
Mary Creagh told Daybreak she was "looking at a better system that provides value for money for the taxpayer" but would not elaborate beyond that.
Despite numerous questions on whether to bring the railways back under government control, she could only would say "we need to look at the laws governing the railways," as those had not been changed since 1993, when the network was first privatised.
Many passengers took a poor view of rail fare increases today as annual season tickets rose by an average of 3.1 percent.
Simon Jones, who was travelling to Newcastle from London King's Cross this morning, said:
It's a lot of money for a poor service. Fares are pretty high. My salary has just gone up 1 percent but fares are rising around 3 percent. There are delays on practically every day.
Ben James, who was also travelling from London to the north-east, said:
We're not really getting value for money. At Clapham Junction (in south London) you can hardly get on a train.
Andy Stewart on the ITV News Facebook page said fail fares were a "rip-off":
Train fares are a total rip-off! It's cheaper to fly from Edinburgh to London, allowing for getting out to the airports.
The Government insisted that it understands passengers concerns over the cost of rail fares as annual season tickets rose by 3.1 per cent.
Campaign groups have complained about the increase, with the Campaign for Better Transport saying that fares are rising three times faster than wages.
A Department for Transport spokesman said: "The Government understands concerns rail passengers have about the costs of fares and the impact they have on household budgets.
"That is why next year, for the first time in a decade, regulated fares will not rise on average by more than the rate of inflation, offering relief for families and the hard-working people.
"As a result of the economic policies that this government has put in place, the most recent forecasts from the Office for Budget Responsibility are that by around 2015, fares will be rising in line with wages and salaries."
The spokesman insisted that the fares passengers pay will drive the "biggest programme of rail modernisation ever" resulting in new state-of-the-art trains, better stations and shorter journey times.
The latest rail fare price rise will mean increasing financial pain for commuters, a campaign group has warned.
Annual season tickets have increased by an average of 3.1 per cent, meaning some passengers will have to pay up to £5,000 per year for their travel.
Bruce Williamson of the campaign group Railfuture, said: "This latest fare rise comes after 10 years of inflation-busting fare increases, meaning that our trains are easily the most expensive in Europe.
"There's no doubt that this will mean increasing financial pain for many ordinary commuters who are facing a cost of living crisis."
Travel choices and employment opportunities will be harmed if the cost of transport continues to rise, a charity has warned.
Commuters will now pay higher rail fares after annual ticket prices rose by an average of 3.1 per cent.
Jason Torrance, policy director of sustainable transport organisation Sustrans, said commuters would still feel the effect of the price rise.
"The Chancellor's move to bring an end to the inflation-busting fare rises we've seen over the last decade shows a recognition that rising transport costs are a barrier to economic recovery.
"But commuters will still feel the pinch this new year because salaries aren't increasing by anywhere near the level of inflation.
"If transport remains so prohibitively expensive, we will continue to restrict travel choices and opportunities to access essential services and employment."
Passengers will pay higher rail fares from tomorrow, with annual tickets rising by an average of 3.1 per cent.
The increase will mean some commuters will be forced to pay more than £5,000 a year, with annual tickets to London from Deal and Dover Priory costing £5,012.
A number of these fares, including some on the East Coast route, are going up by much less than 3.1 per cent, with the overall rise in tickets - regulated and unregulated - being 2.8 per cent.
The increase also means some annual season tickets will break the £4,000 mark, with a Basingstoke-London annual fare now costing up to £4,076.
The rise is for regulated fares which include season tickets.
The increase could have been even greater, but Chancellor George Osborne announced in his Autumn Statement in early December that the regulated fare price cap of RPI inflation plus 1 per cent was being changed to RPI plus 0 per cent.