Six early morning rail services - serving Wigan - have been scrapped due to a shortage of drivers.
Northern has confirmed that the cancellations of the 7.36am and 8.36am Liverpool Lime Street to Blackpool North, the 8.30am Preston to Liverpool Lime Street and the 7.24am Manchester Airport to Blackpool North train, which all call at Wigan North Western, have been axed due to staffing difficulties.
Serious delays have also been caused to three other services running between the resort and the city centre, affecting North Western passengers.
The travel chaos has come on the first working day after the May timetables change took effect on Sunday.
Wigan MP Lisa Nandy said on Twitter: "Chaos on Northern Rail again this morning. This franchise is failing and must be removed."
One passenger, Deborah Fairhurst, said the 6.23am service from Wigan to Manchester Oxford Road had been axed, along with the 6.44am train from Gathurst to Manchester, and the 7.01am from Wigan Wallgate to Oxford Road was "seriously overcrowded" and running an hour late.
Controversy had already been created after the operator diverted stopper services from Manchester Piccadilly to Manchester Victoria.
The rail union RMT has branded the situation "Meltdown Monday.
Mick Cash, general secretary, said: "The union is picking up reports from..Northern... of a hopeless lack of planning, combined with a shortage of crew and fleet, which has reduced the Monday morning journey to a nightmare for many passengers.
"It is our members dealing with the anger at the sharp end not the well-paid top brass from Arriva , who are responsible for this Meltdown Monday on our railways."
A Northern official, posting on their website, has confirmed that the cancellations have been due to drivers shortages and advised passengers to seek redress from their 'Delay Repay' scheme online.