First imposed record increases this month on passengers travelling between London and dozens of stations north of the capital. Cheap day returns are no longer valid between 4.30pm and 7pm, forcing people to buy much more expensive standard returns.

Fares between St Albans and London have increased from £7.90 to £14.50 for people who want to travel home during that 21⁄2-hour period.

Similar increases are being proposed for South West Trains, the largest franchise, which carries 140 million passengers a year on lines between Waterloo and the South Coast.

Ministers remained silent about First?s announcement while London TravelWatch, the official passenger watchdog, accused it of ?blatant profiteering?. But The Times has learnt that the fare increase was the result of a secret agreement last year between the Department for Transport and First.

Alistair Darling, who was the Transport Secretary then, announced that passengers would benefit from a series of improvements but failed to mention the plan to raise fares.

Mr Darling said that his decision to award the Thameslink/Great Northern franchise to First would ?deliver better services to passengers?. He continued: ?There will be increased capacity into London during peak times, enhanced facilities for passengers on board trains and at stations and reliability will improve.? Mr Darling made no mention of fare increases even though First had made clear to the department that the £800 million it was paying over nine years to run the franchise depended on restricting cheap tickets.

A spokesman for the department said: ?We accepted that this was a good commercial solution to the problem of overcrowding.?

He admitted that the department had not been as transparent as it could have been but the decision about when to make the increase had been left to First.

Asked whether similar increases would be imposed at South West Trains, the spokesman said: ?We are open to any innovative solutions which can reduce overcrowding on SWT.?

Brian Cooke, the chairman of London TravelWatch, said: ?It was devious of the Government not to make clear what had been agreed in First?s bid. Ministers wanted First to do their own dirty work. When a franchise is agreed, the Government should immediately publish all of the terms, not just the attractive bits.?

Mr Cooke said that it would have been far better to deal with overcrowding by adding extra carriages to trains rather than pricing people off afternoon and evening services.

Malcolm Ginsberg, a regular rail user between Potters Bar and London, said that First had not only reneged on promises to lengthen trains but also had reduced some services from eight carriages to four. ?It was outrageous of the Government to approve the increase without telling us,? he said.

?Making the railways unaffordable for many people is a very crude way of dealing with overcrowding.?

A spokesman for First, which has rebranded the Thameslink franchise as First Capital Connect, said that it expected to reduce the number of passengers on trains between 4.30pm and 7pm by 13 per cent. First will announce today a partial retreat by reducing the number of stations affected from 37 to 27.

The previous rules on the use of cheap fares will be reintroduced at Cuffley, Bayford, Watton at Stone, Brookmans Park, Welham Green, Radlett, Hatfield, Hertford North, Welwyn Garden City and Potters Bar.

A train company bidding for the new South West Trains franchise said: ?It is highly likely that similar increases will be considered on some routes from Waterloo.?