Transport Focus urged all operators in Britain to introduce a so-called yellow card system to “make things fairer for everyone”.
A record of passengers found not to have the correct ticket or railcard would be taken so it can be checked in future.
This comes in the wake of cases where passengers were being prosecuted over small amounts of money were highlighted in the media.
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Engineering graduate Sam Williamson said he feared getting a criminal record and being fined hundreds of pounds after being told he was being prosecuted by Government-owned operator Northern because he unknowingly used a railcard at the wrong time, resulting in a £1.90 underpayment.
Northern dropped its action against him following media coverage.
What is the Penalty Fares system?
Train operators also used the Penalty Fares system which is a £100 penalty plus the price of the full single fare applicable for the intended journey.
If paid within 21 days, the Penalty Fare is reduced to £50 plus the price of the single fare.
Industry body the Rail Delivery Group previously estimated that around £240 million is lost through fare evasion on Britain’s railways each year.
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Other approaches suggested by Transport Focus to tackle the issue include introducing a digital database of railcards to allow ticket inspectors to check a passenger’s eligibility for a discount if they say their railcard has been forgotten or cannot be loaded on a phone.
The watchdog also wants increased measures to collect fares so passengers know they will be asked to produce a valid ticket at the start and end of their journey as well as during it.
It said there are “clear benefits to having safe, secure stations with proper barriers”.
Natasha Grice, director for rail at Transport Focus, said: “Transport Focus has long been concerned about the complexity of rail fares and ticketing, particularly for passengers who find it hard to buy the right ticket for their journey.
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“We understand and support the principle that all users of rail should be paying for their ticket, but we want to make sure that passengers who make an innocent mistake aren’t punished unfairly.
“There are some things that the industry could do now to make things better, and our research tells us that if the railway is to build trust and confidence, an improved approach to revenue protection is needed.
“Recouping this money could help boost investment in services, making things better for passengers.”
In November, the Department for Transport ordered regulator the Office of Rail and Road to carry out an independent review of rail fare prosecutions and enforcement.