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The 5.9% average increase is higher than the Retail Prices Index (RPI) measure of inflation, which was 5.2% in November.
Season tickets will rise by an average of 6 % - taking the cost of a yearly ticket to London to more than £4,000 for a number of towns, including Hastings, Eastbourne and Bedford.
Michael Roberts, chief executive of the Association of Train Operating Companies (Atoc) said that the money raised via higher fares would help pay for new trains, faster services and better stations.
"The long-standing Government approach to sustaining rail investment is to cut the contribution from taxpayers and increase the share paid for by passengers," he said.
"The industry is working together to continue cutting costs as a way to help limit future fare rises and offer better value for money for taxpayers over the longer term."
Passenger groups responded angrily to the news, which has come at a time when one in eight trains (13 per cent) run late, there is widespread overcrowding and disruption to Christmas services due to engineering works.
Sophie Allain, of the Campaign for Better Transport, said: "Another New Year approaches and yet another round of eye-watering train fare hikes looms. We still have the highest fares in Europe."
Manuel Cortes, leader of the TSSA transport union, said: "Once again we have the private train operators defying all economic logic and increasing the squeeze on passengers during a recession."