Wigan MP Lisa Nandy claimed emails from the Department for Transport (DfT) which had been handed to her show that ministers and officials were warned in 2015 about "impending chaos" on the region's railways.
The messages show that campaigners warned the reduction in the number of services between Southport and Manchester Piccadilly from May 20 would have a "very serious detrimental effect".
One email published by Ms Nandy states that in correspondence between DfT officials it was stated that the Leeds to Southport connection is "not really valued".
In another, a DfT official wrote to Transport for Greater Manchester describing a "classic handling strategy", whereby they would encourage the "myth" that services were being closed entirely so that "people will rejoice" at the news that they are merely being diverted.
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The message was signed "Yours cynically".
Shouts of "resign" could be heard from some Opposition MPs as Ms Nandy read out some of the information before questioning if Prime Minister Theresa May was "so incompetent" that she "literally has not got a clue what is going on in her Government".
Mrs May declined to comment on leaked information, adding the DfT was advised by an independent panel over timetable changes.
Thousands of passengers have suffered following the introduction of new timetables, including those travelling on Northern and Govia Thameslink Railway (GTR).
Speaking during Prime Minister's Questions, Ms Nandy said: "After four weeks of Northern rail chaos, passengers in the north of England have had enough.
"The Government has said Network Rail didn't deliver and Northern wasn't prepared.
"But I have been handed emails from within the Department for Transport that show ministers and officials were warned of impending chaos as long ago as two years ago.
"These emails are a disgrace.
"In them, officials describe key northern routes as valueless, discuss classic handling strategies for Members of Parliament, discuss whether to throw a sop to Northern passengers groups, and debate whether to propagate myths in order to divert public attention from agreed planned route closures."
Ms Nandy added: "Will the Prime Minister explain to this House why she has withheld this key information from us and the public, or is she so incompetent she literally has not got a clue what is going on in her Government?"
Mrs May replied: "No government responds across the despatch box to leaked documents that they have not seen.
"Can I also say to (Ms Nandy) in advance of the timetable changes that took place for both Northern and Govia in May, there was a separate independent panel set up by the DfT to reassure the Department for Transport about the the nature of those plans.
"She may shake her head but that independent panel was set up and advised the Department for Transport."
A DfT spokesman said: "These emails are nothing to do with the current timetabling issues being endured by Northern.
"The emails are more than two years old and relate to the wider design of the Northern franchise and deciding which trains were most needed to best serve the passengers in the region.
"The excerpts quoted relate solely to a decision over whether trains from Southport would stop at Manchester Piccadilly or Manchester Victoria and have no further implications beyond that individual route.
"It is deeply regrettable that a DfT official used inappropriate language and that matter is being looked at."