Lisa Nandy raised the issue at Prime Minister’s Questions, saying the leaked messages “show utter contempt” for passengers.
It comes as thousands of passengers battle a major shakeup of train timetables on Northern and Govia Thameslink Railway, which has seen widespread delays and cancellations as operators try to adapt to the changes.
She said officials at the Department for Transport had described key routes as “not really valued” and talked about “spreading false information” to distract attention from route closures.
The MP for Wigan said the information was included in emails which had been handed to her.
As she read out details from the emails there were cries of “resign” in the chamber, directed at embattled transport secretary Chris Grayling.
Ms Nandy then asked if Theresa May was “so incompetent” that she “literally has not got a clue what is going on in her government”.
The prime minister said in response that “no government responds to leaked emails it has not seen”.
Asking her question at PMQs, 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 said in response: “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 nature of those plans.
“She may shake her head but that independent panel was set up and advised the Department for Transport.”