Transport Secretary Chris Grayling has ordered an investigation after reports rail firms “misled” customers.
The watchdog Transport Focus said companies were selling tickets for services over Christmas, despite knowing they will not run.
Mr Grayling said was “unacceptable” for passengers to have to pay higher “walk-up” fares at Christmas.
Industry body the Rail Delivery Group said its members would “develop a plan” to address the complaints.
Mr Grayling said: “It would be totally unacceptable if any passenger has to pay walk-up fares this Christmas because advance tickets were not available.”
“I expect passengers to be offered the highest standards of customer service and have ordered an immediate investigation into this report.”
He also urged Network Rail and train companies to closer together to minimise disruption and make sure the problem did not happen again.
Transport Focus found more than 2,600 incorrect journeys – those already cancelled or scheduled to face disruption – were on offer during the Christmas week alone.
The group also found that by 13 October – 11 weeks before Christmas – reservations had not opened on Great Western, London Midland, South Western Railway and Southern – despite regulations stating they should.
Only 15% of services were open for reservation on Greater Anglia and 25% on Virgin Trains.
Transport Focus chief executive Anthony Smith said: “Failure to release timetables 12 weeks ahead of travel can mean passengers buy tickets for trains that will not run.
“That can’t be right. Train operators’ advice is to book early at Christmas to get the best deal.
“But if the timetable has not been finalised only more expensive ‘on the day’ tickets can be bought.”
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Helen Firth, 37, from Surrey commutes to London for work and says getting home on time to see her nine-year-old son was important.
But she said she was unable to plan her Christmas journeys.
“It’s unfair if someone’s forked out a bunch of money, but don’t know if their train will be delayed,” she said.
“Companies should at least advise people so they have the option of knowing and planning other routes.”
Paul Plummer, chief executive of Rail Delivery Group responded to the Transport Focus criticisms, saying the issue was “important” and he would reply more fully before Christmas.
Transport Focus have called for a network-wide review to ensure train operators publish correct timetables 12 weeks in advance.
They also want incorrect information to be removed from online timetables, and say passengers who have already bought tickets must be notified when there are changes to their journeys.