Train company Northern and Network Rail are to commission an independent report over recent disruption to services.
Passengers have faced widespread cancellations and delays, prompting calls for an investigation into Northern's "unacceptably poor" service.
The mayors of Greater Manchester and the Liverpool City Region also called for the company to lose its franchise if improvements are not made.
Network Rail said the new report would "ensure lessons are learned".
Northern has apologised for the disruption and said it was the result of a timetable change on 20 May.
'Tough for customers'
Managing director David Brown said: "There is urgent work to do to fully understand what did and didn't work on all aspects of planning and delivery of the new timetable."
Martin Frobisher, managing director for Network Rail's London North Western route, said: "We recognise how tough it has been for customers, particularly since the May timetable change last weekend and we're sorry for that.
"We are working hard with Northern to get service back to where it needs to be.
"The independent report will ensure lessons are learned and that there are no repeats of current problems."
Many Northern staff members held a 24-hour strike on Thursday in an ongoing dispute about safety involving driver-only operated trains, with a further strike planned for Saturday.