On 33 out of a sample of 50 journeys, it is possible to obtain a cheaper fare than the one advertised on nationalrail.co.uk - which describes itself as the "definitive source of customer information" - an investigation by The Times found.
Savings can be made by splitting tickets, where a passenger buys several tickets for destinations along their route rather than one for the entire trip.
One of the most startling examples uncovered was an Anytime Single from Penzance to Birmingham, changing at Plymouth.
The published fare is £149.30, but it is possible to pay £85 less for the same trains by split-ticketing.
The investigation also found some operators are not correctly labelling train station ticket machines to ensure passengers know only a limited range of tickets are available from them.
At least half of the 63 machines in London analysed by The Times were either not labelled or "featured scant information" about the range of tickets they sell.
New rail minister Paul Maynard said he is "already looking at" the issue of how train tickets are sold, and insisted that "passengers should always be able to get the best deal".
He went on: "The industry must work harder to make this a reality.
"Train operators have made some improvements and passengers are benefiting from better on-screen information at some stations, but there has got to be improvement right across the network.
"I will be raising this with the Rail Delivery Group (RDG) that represents all train operating companies as a priority. Passengers deserve better."
An RDG spokesman said rail firms have updated 95% of the 2,500 ticket machines around the country with either stickers or better on-screen information.
He acknowledged it can "occasionally" be cheaper to buy more than one ticket for a journey, adding that train companies are "looking at ways to make buying tickets simpler".
He went on: "We want customers to get the right ticket for their journeys at the best price. We recognise that different types of tickets and fares can be confusing and we want to make things as straightforward as possible for customers. We know that we have more to do.
"Train companies offer a range of good value fares, one of the reasons why passenger numbers have doubled in the last 20 years. We're working hard to make buying train travel simpler and to give passengers better information."