Northern launched an eight-week interim timetable on Monday, removing 165 trains - six per cent of its services.
Northern's policy is for passengers to only claim compensation based on the alternative timetable rather than previous versions.
The reduced timetables failed to stop Monday becoming the start of a third week of rail chaos for passengers.
Even before the new timetables, Northern services suffered frequent delays and cancellations.
We want to hear from you about whether your journey has been blighted by delays or cancellations as we run a live blog documenting the region's rail travel.
It comes as the Mayor of Greater Manchester Andy Burnham said frustrated train commuters in the North should get substantial compensation and fare reductions, claiming Northern is in the "last chance saloon".
In a letter to the chairman of Transport for the North (TfN) John Cridland, the mayor said Northern is likely to benefit financially from the operation of the reduced timetable and if the company is not prepared to fund the compensation package and reduce fares voluntarily, then fines should be imposed to pay for it.
Northern insists it will still run more trains than it did before last month's timetable change, and expects to get back to a full timetable service by the end of July.
The firm's managing director David Brown has apologised for the "unacceptable service", and said they are working hard to fix the problems.