TransPennine Express has suffered problems for several months because of staffing issues. The company today said there was a high level of unplanned cancellations and disruption due to a "significant" issue with the rostering system.
A train operator which runs services across northern England and into Scotland has issued a "do not travel" alert as a "system issue" is causing major disruption on its network.
TransPennine Express (TPE) said there was a high level of unplanned cancellations due to a "significant" issue with the rostering system.
The issue was caused by an overnight fault affecting rostering software designed to ensure workers and trains are in the correct location at the right time to run services.
It expects to cancel around a third of the 325 services planned for Wednesday.
TPE admitted that this will have a big impact on customers and has apologised.
The operator has advised them not to travel on TPE and to use alternative transport.
TPE said it does not know when the problem will be resolved, and disruption is expected to continue for the rest of the week.
'Government needs to step in'
Greater Manchester Mayor Andy Burnham wrote on Twitter: "This can't carry on. The government needs to step in - now."
And Labour's shadow transport secretary, Louise Haigh MP, said: "This fiasco is causing untold damage and ministers are missing in action.
"After 12 years, the Conservatives have left the north with crumbling infrastructure and failing operators. Enough is enough, passengers have been taken for a ride for too long.
"It's time for ministers to finally hold operators to account for appalling performance, and a failure to recruit and invest in the long-term future."
Company spokesperson Kathryn O'Brien said: "Due to a significant rostering system issue, today we are experiencing a high level of unplanned cancellations and disruption across our network.
"We know this will have a significant impact on customers travelling with us today and sincerely apologise for any disruption caused."
She added: "We are working hard internally and with our system provider to resolve the situation as soon as possible.
"We are doing all we can to keep customers on the move but while problems persist, we advise customers not to travel and to seek alternative means of transport."
The company's routes include Liverpool to Edinburgh via Manchester, and Liverpool to Glasgow.
TPE, which is owned by FirstGroup, has suffered problems for several months because of staffing issues.
The operator has previously blamed a combination of problems, such as high levels of train crew sickness and a training backlog, for causing prolonged disruption.
It has also been hit by workers not volunteering to do paid overtime on rest days and infrastructure faults.
TPE workers who are members of the Rail, Maritime and Transport union (RMT) and Aslef are repeatedly striking in long-running disputes.
Anthony Smith, chief executive of watchdog Transport Focus, told the Commons' Transport Select Committee earlier this month "the industrial relations issues have been very corrosive and have clearly undermined (TPE's) ability to provide a reliable service".