For example, in Britain long-distance turn-up-and-go fully flexible day-return fares to the principal city (London) were 87% more expensive than in the next most expensive country surveyed - Germany.
This type of British fare was also more than three times as expensive than in the cheapest country surveyed - the Netherlands.
British annual season tickets for journeys of no more than 25 miles were 88% more expensive than the next most expensive country - France - and more than four times pricier than the cheapest country - Italy.
ANNUAL SEASON TICKET
Passenger Focus, averages for journeys of 11 to 25 miles
However, most British passengers appeared better served than other European passengers by the number and times of trains available, Passenger Focus said.
A previous survey by the watchdog found that most (83%) of British passengers were broadly happy with the quality of rail services.
But under half (43%) were happy with the value for money they were getting.
Looking at long-distance journeys, the report said the underlying fares structure was "complicated and not logical" and had to be seen to be fairer to passengers.
Passenger Focus said the government should reconsider its plan to shift the cost of funding the railway from taxpayers to passengers, arguing that the policy was "born in very different economic times".
Spokesman Guy Dangerfield told the BBC: "During a period of recession, it is untenable to continue with above inflation fare increases.
"The consequences for passengers are too severe."
Lord Adonis said the government was committed to "sharing the cost of rail services fairly between taxpayers and passengers".
"It is estimated it would cost taxpayers an extra £500m a year to bring UK commuter fares in line with these other European countries, which are more heavily subsidised," he said.
"There is no free lunch here. We as a community pay for this one way or another."
He argued that since 1997, regulated fares had fallen sharply relative to earnings, and that with inflation now falling, train fares would drop further.
He added: "The Conservatives' plans to cut £840m from the Department for Transport budget would mean cuts to rail subsidy and therefore an increase in the fares paid by passengers."
But Shadow Transport Secretary Theresa Villiers said: "Under Labour, passengers have been forced to put up with eye-watering fare hikes in return for overcrowding levels that exceed 170% on the worst services - so it's little wonder they feel they are not getting value for money on Labour's railways."
Michael Roberts, chief executive of the Association of Train Operating Companies, said the report highlighted "many positive features for passengers".
"Train operators have worked hard to deliver on the things that matter to passengers, including a range of great fare deals to suit different pockets," he said.
"But operators remain committed to doing more. An additional 1,300 vehicles in the next few years will help tackle overcrowding and we are already working with Passenger Focus and Network Rail to improve passenger satisfaction with the information provided during disruption."
Transport commentator Christian Wolmar said there appeared to be flaws at the very heart of the British system.
"Under British Rail, we didn't get much subsidy into the rail system. Now we get an awful lot of subsidy into the rail system and yet the fares are still high," he said.
"There is something fundamentally wrong there and I think this research highlights that."
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