This means the cost of a Brighton to London 12-month season ticket going up by £148, a price hike of £140 for an annual ticket for journeys from Gloucester to Birmingham and a rail fare increase of £108 for a year-long Liverpool to Manchester season ticket.
Ministers are considering using the consumer prices index (CPI) to set fares in a move that will dramatically cut the size of future increases and align them more closely to the cost of living.
Regulated fares, which includes season tickets, and unregulated fares, such as off-peak leisure tickets, will go up by an average of 3.2% from 2 January, the largest increase since 2013, when fares rose 3.9%.
The Rail Delivery Group, the industry body made up of the train companies and Network Rail, said more than 97p in every pound from fares went back into "improving and running" the railway.
The RMT Union called the announcement "another kick in the teeth for British passengers", with general secretary Mick Cash saying the United Kingdom pays the highest fares in Europe.
The passenger watchdog Transport Focus compared the news of the price rises to "a chill wind blowing down platforms", adding: "Many passengers face stagnant or falling incomes while rail fares continue to climb".
Fewer than half (47 per cent) of passengers are satisfied with the value for money of train tickets, according to Transport Focus.
Manuel Cortes, general secretary of the Transport Salaried Staffs Association, warned that rail users were being "bled dry to ensure our private train companies stay in profit".
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Chief executive Paul Plummer noted that the Government controls increases to nearly half of fares while the rest are "heavily influenced" by the payments train companies make as part of contracts to run franchises.
"Alongside investment from the public and private sectors, money from fares is underpinning the partnership railways long-term plan to change and improve".
Successive governments have looked to cut taxpayers' funding of railways and increase the contribution from passengers.
The increase was criticized by passenger groups as well as the train union representing rail workers which said fares remained the highest in Europe.
It warns passengers are already struggling, with the average growth in wages failing to keep up with the pace of hikes.
Rail fares had increased on average by 2.3% this year, while they had risen by 2.8%, 2.2% and 1.1%, in 2014, 2015 and 2016 respectively.
"Delayed, cancelled and overcrowded trains are what springs to mind when many commuters think of their rail journey, so to ask them to pay a significantly increased fare for a poor service is wrong".