The last bastion of cheap rail travel, the saver fare, is under threat as the government considers changes that will make some off-peak trains more expensive.

The suggested changes would mean that travelling just after the peak morning period and in the late afternoon becomes costlier, under proposals being discussed by the Department for Transport, train operators and the rail watchdog Passenger Focus.

The talks are taking place against a backdrop of mounting passenger anger over year-on-year price rises and overcrowding on trains, with passenger groups warning that the government is in danger of driving people off the railways.

A saver return from London to Manchester on Virgin Trains costs £59.50 and is controlled by a price cap, with the unregulated standard open return costing £219. Under the proposals, the cheaper saver ticket will become more expensive for travel closer to peak hours.

Long-distance operators such as GNER, Virgin and FirstGroup want to introduce a new price tier because services near peak hours - around 9.30am, 3.30pm and 7pm - are becoming overcrowded with saver ticket buyers. In return, train operators are willing to make the changes "revenue neutral" by cutting the price of some peak tickets and guaranteeing that some saver fares - typically a third of the cost of a full fare - will not be increased.

Colin Foxall, chairman of Passenger Focus, warned that it would be a "great shame" if railway staples such as the cheap day trip were endangered. "The government wants to see people using trains and it needs a system that preserves an affordable walk-up fare," he said.

Richard McClean, operations director of GNER, said allowing train companies greater flexibility with ticket prices would "smooth out" overcrowding problems. "It's not about putting fares up in the shoulder of peak hours, it's about balancing demand and supply in a way that provides a better service."

Price caps on tickets are under pressure amid record demand for rail travel and government belief that the fare payer should make a greater contribution to the multibillion-pound cost of maintaining the rail network. Saver fares accounted for 7% of the 1.1bn rail journeys last year.

A spokesman for the DfT said: "We have always said that we are in the business of encouraging more people to use the railways. DfT, Passenger Focus and Atoc [the Association of Train Operating Companies] are working together as part of the review of regulation of saver fares but no decisions have yet been taken."

Atoc, which is leading negotiations on behalf of train operators, said it wanted a "formula for a much more simplified fare structure", which would include the deregulation of saver fares.

Any move to lift price caps is likely to incur the wrath of passengers - only four out of 10 rail users believe they get value for money for their ticket.

The DfT will publish its five-year plan for the railways in the summer, outlining its vision for the network for 2009 to 2014. Network Rail, the company that owns and maintains the rail system, is asking for up to £29bn in funding over the period.