Fare rises by Arriva Trains Wales and South West Trains are not excessive, according to a rail watchdog.
The companies faced criticism over the changes which mean some off-peak passengers face rises of up to 34%.
The Office of Rail Regulation (ORR) said the increases were unwelcome to the travelling public but it was "not appropriate to open an investigation".
Customer group Passenger Focus said it would challenge the ruling in order to protect people from huge price rises.
Anthony Smith, Passenger Focus chief executive, said: "What this ruling seems to imply is that off-peak passengers are left totally unprotected against unreasonable fare rises.
"The assertion by the ORR that people have a choice simply does not ring true.
"We will challenge this ruling in an attempt to give off-peak passengers some protection against massive price rises."
SWT said the new prices would bring the company into line with other operators and Arriva said it was offering "new attractive prices" for long distance travel and encouraging advance booking.
Examples of the SWT's increases, which were first announced in March, include a cheap-day return from Alton, in Hampshire, to London rising from £15.80 to £19 - a 20.25% increase.
A Bournemouth-to-London cheap-day return will go up from £36.40 to £43.70 - a 20.05% rise.