The company cancelled around 80 services across its network, mainly affecting Liverpool, Lancashire and Greater Manchester.
Northern apologised to passengers affected by the disruption, saying in a statement: "Some of our staff have made themselves unavailable for work on Sunday and operational teams have been working hard to make the best use of available staff and bring others in where possible."
Mick Cash, general secretary of the Rail, Maritime and Transport (RMT) union, said: "It is outrageous for Northern Rail to try and lump the blame for the crew shortages that led to widespread cancellations yesterday on their workforce.
"It is a scam to try and cover up the fact that they simply don't hire enough workers to fill their rosters.
"This garbage about 'staff making themselves unavailable' is a twisting of words that is positively Trumpesque and our members are rightly angry at the suggestion that the service chaos on successive Sundays is somehow down to them and not the company which has repeatedly shown itself as unfit to run a railway.
"They should be stripped of the franchise and the Northern routes should be nationalised."
Rail replacement buses were used, and an amended timetable for trains was put in place.
Mick Whelan, general secretary of the train drivers' union Aslef, said: "Numerous times we have sought to put Sundays in the working week, which would have obviated this issue.
"The company, though, prefers to run on voluntary overtime rather than employ enough staff to operate the services it promised in its franchise application to deliver for passengers.
"Then, of course, it seeks to blame those who opt not to work their days off. That's a bit rich, and the company, by this attitude, runs a serious risk of alienating drivers even more and losing the little goodwill it has left with an increasingly demoralised workforce."
A spokesman for Northern said: "We actually have more drivers than we need to run a full timetable in normal circumstances. We currently have 1,529 train drivers, 180 more than when we started the franchise."