The Strategic Rail Authority (SRA) said the review was needed to tackle over-crowding on some routes and a lack of revenue across the service.
The authority's chairman Richard Bowker has said "some tough decisions have to be made" on pricing and that one option could be to raise fares on the busiest lines at the busiest times.
Transport 2000, the environmental transport group, said it was "outrageous" that the SRA's response to over-crowding was to force people off public transport by rising prices.
"This is not the way rail policy should be heading," said spokesman Steve Hounsham.
"The railways must expand to deal with over-crowding, not force people into cars."
'Unregulated increases'
Transport 2000 said the consultation was "a once in a blue moon opportunity" to change the rules governing fares for the benefit of passengers.
The Rail Passengers Council called for a full consultation with rail users and also warned "unregulated" increases would "drive people off the railway and onto the roads".
"What we don't want to see is an assumption that fare rises are an inevitable consequence of this review," said spokeswoman Caroline Jones.
"Passengers can't be expected to pay for improvements they haven't yet seen."
The SRA said the cost of running the railways had risen significantly since privatisation.
But fares currently account for just over half the operating costs of the railway.
Paying for the trains
Operating costs have risen
Many fares are capped
Fares account for just over half the costs of the railway
How is the other half to be paid for?
It added that for the last six years many commuters have benefited from a cap on fare rises, which has kept prices 1% below inflation.
The authority has now said these caps may have been contributing to overcrowding, and that perhaps it should change its policy.
While one answer could be to charge more on popular routes, another could be to cut the price for off-peak commuter tickets, to encourage passengers to travel when it is quiet.
Fares 'a mess'
In London, commuter fares are currently linked not only to an inflation formula, but also to individual train company performances - which means they have not risen significantly in recent years.
The SRA has said this could change, as the "existing automatic link between fares and performance has not worked well".
The Rail Users Group described the existing fare system as "very complicated".
"People don't know how much they're going to pay for a particular journey and they're finding it hard to judge value for money," director Anthony Smith told BBC Radio 4's Today programme.
"We've also seen some substantial fare increases across the network.
"It's a mess."
Discount travel
Off-peak, turn-up-and-go saver fares on long distance trains are being reviewed, and again there is a possibility prices may go up to reduce overcrowding.
The introduction of a new National Travelcard is also being considered - offering discount travel across the country.
Fares likely to rise
Peak-time tickets on busy commuter lines
Turn-up-and-go long distance saver fares
The SRA said that although £33.5 billion of public money had been committed to the railway, more might be needed, and the issue was where this was to come from.
The authority is publishing a consultation document - the biggest review since privatisation of how train travel is paid for - on Friday and launched a three-month consultation period.
The authority's chairman Richard Bowker said he had the problem of wanting to get more people onto trains, while at the same time having to reduce overcrowding.
But he said no decisions would be made until summer 2003, and changes would not come in until 2004.