Northern is implementing increases of up to 50p from 21 May to "bring fares in line with other areas".
The RMT union said the "latest fares rip off is just another example of costs being shifted" to passengers.
Northern, which has introduced rises since September 2016, said fares in the area have been "historically low".
The rail operator said there would be an increase "of no more than 50p" on the majority of off-peak day returns and singles for journeys made within Greater Manchester.
It said there would be no change to anytime day single, anytime day return or weekly season tickets and Transport for Greater Manchester concessions.
There would be reductions on some tickets, it added.
Northern said the rises were to make fares "fair and consistent" across the network.
RMT general secretary Mick Cash said: "This latest fares rip off is just another example of industry costs being shifted to the passenger."
Rochdale councillor Andy Kelly said the hike was "the great rail rip off " and would "affect the poorest".
"Many commuters tell me that they have changed their shift patterns to take advantage of off-peak discounts."
Northern said the travel increases would go towards its modernisation programme which will see it get rid of Pacer trains by 2020.
Rail workers on Northern, Southern and Merseyrail have gone on a number of strikes with the latest on 8 April over proposals for driver-only-operated trains.
Rail fares for some off-peak Northern services in Greater Manchester will be increased by up to 10% - the third rise within the past year.