Rises in rail and Tube fares have taken effect with some mainline season tickets going up almost 13%.

Passenger groups have reacted with fury to the rises but the Government and London mayor Boris Johnson say the increases are necessary to support vital transport projects.

Overall, main line fares are rising by an average of 6.2%, with regulated fares, which include season tickets, going up by average of 5.8%.

But as these are just the average rises, some fares are going up by far more than this.

On services run by the Southeastern train company, regulated fares are allowed to rise by an average of 7.8% to account for extra investment in the franchise, including the high-speed Javelin trains. This means a Ramsgate-London season ticket goes up 12.8% to £4,376, while an Ashford International-London season ticket rises 12.7% to £4,328.

Other passengers facing above-the-average increases from today include those travelling on services run by the Southern train company between Haywards Heath and London where season tickets are going up 7.69% to £3,304. A season ticket between Brighton and London on Southern rises 7.68% to £3,532.

The 5.8% average main line rail increase in regulated fares (which include season tickets) is based on the July 2010 retail prices inflation (RPI) figure of 4.8% plus 1%, with train companies allowed to use "flex" (flexibility) to average out the increase.

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. For many passengers, this flexibility won't appear fair.

"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."

A spokesman for the Association of Train Operating Companies said: "The RPI flex has existed since privatisation and was waived in 2009 by the Government but, as expected, it has now been reinstated by the Department for Transport.

"The average increase allowed in January is RPI plus 1%. Any fare increased by more than this must be balanced by another fare reducing by the same amount. The use of flex means that some fares will go up by less than 1%. Importantly, the average is weighted so that operators cannot increase fares on routes with lots of passengers, and likewise reduce them on routes with fewer passengers."