Clare Waller, Network Rail’s area director for Manchester, apologised to passengers, saying they had not received “the service they deserve or expect”.
She added: “Our teams have now fixed the damage to the power cables and the railway lines are reopened, but it will take some time still to get train services back to normal.”
Earlier, Chris Halpin, from Network Rail, told Radio Manchester that the closure had prevented empty trains from returning to depots overnight, causing knock-on delays.
He warned the timetable would be disrupted for much of Friday but said services were not expected to be affected on Saturday.
Routes affected included services between Manchester Piccadilly and London Euston, Sheffield, Crewe and Stoke-on-Trent.
Passengers can use their tickets on alternative train services, Bee Network buses and Metrolink trams while disruption continues, Network Rail said.
Network Rail has urged passengers to check National Rail Enquiries and allow extra time for travel.