Severe delays and cancellations on the first working day of a new timetable have led to fresh calls for action on northern railways, including stripping the rail operators of their franchises.

The worst disruption came on TransPennine Express, where almost 50% of early trains were cancelled or more than half an hour late, followed by Northern, which had almost one in 10 services seriously disrupted among a total of one in three delayed by mid-afternoon on Monday.

Train operators insisted that the disruption was unrelated to the introduction of a new timetable, after taking steps to avert the problems after a previous changeover 18 months ago.

On Monday, passengers faced staff shortages, signalling problems, train faults and ongoing industrial action.

Andy Burnham, the mayor of Manchester, said the rail disruption had gone on far too long. “If the government is serious about supporting the north, then it needs to show it by acting this week to sort out our failing rail services.

“As a first step, it should strip Northern of its franchise. That would send a clear signal to all rail operators – notably TransPennine Express – that we will not accept a second-class rail service for people in the north. If TransPennine Express fails to respond to that message, they should be next.”

Andy McDonald, the shadow transport secretary, said ministers had “stood by for years as Northern failed to recruit and retain enough staff and cut services”. He said that after another “botched timetable introduction” there was a responsibility to hold Northern’s owner, Arriva, to account.

Northern said that very few of its 2,800 daily services had changed because of the timetable, and that the “relatively small” disruption was because of operational issues, including driver sickness, signalling failure and train faults.

Industry body the Rail Delivery Group (RDG) said the problems were unrelated to the new timetable and most services were running as planned, at the same level of reliability as a week ago.

TransPennine Express said its delays had been caused by the late delivery of some of its new trains, with a maintenance backlog. It is operating a temporary reduced timetable on routes from Liverpool Lime Street to Edinburgh while it trains up crew for the new fleet.

Some services in the south struggled too in the morning, with continuing strike action on South Western Railway, where half of trains ran late in the morning peak.

Passengers on Great Western Railway were hit by cancellations and delays between Reading and London Paddington due to a signalling fault.

Robert Nisbet, RDG’s director of nations and regions, said: “There are a number of unrelated incidents affecting a small proportion of journeys this morning. More services are running than before the timetable change and passengers will benefit from 1,000 more services a week.”

Anthony Smith, chief executive of watchdog Transport Focus, said: “Passengers don’t care what causes the disruption – they just want things running again as soon as possible, and plenty of visible staff on hand to help them in the meantime.”

Teething problems were in evidence when the timetable came into effect on Sunday, with Great Western Railway and Transport for Wales reporting a number of cancellations and delays.

Train timetables are changed twice a year, in May and December.

A Department for Transport spokesman said the disruption on Monday was “very disappointing” but train operators had assured the department that it was unrelated to the timetable change. He added: “We expect the rail industry to continue to work together to respond rapidly, keep passengers fully updated on their journeys and work hard to ensure performance improves.”