Richard Allan, Deputy Managing Director for Northern, said:
Trains between Leeds and Manchester have been affected by delays this morning.
Broken-down trains and signalling problems, including one near Manchester affecting routes between that city and Leeds, have caused morning rush-hour chaos which also affected those travelling to busy airports for the Easter holidays.
In northern England, trains run by First TransPennine Express between Manchester Airport and Leeds were among those delayed by a signalling problem near Manchester.
Northern Rail was also affected, with delays between Manchester Piccadilly station and Leeds.
Rail workers' union RMT have announced that staff at the Northern Rail maintenance depot at Neville Hill in Leeds are to take a full week of strike action starting on Thursday.
It is the latest step in a continuing dispute over overtime and the grading of roles which staff say do not recognised the "complex and demanding role of this key group of staff".
There was a 48 hour strike in February but, according to RMT the issues remain unresolved and staff will now strike between Thursday April 10 and Wednesday April 16.
Northern Rail maintenance driver members at Heaton and Neville Hill Traincare Depots in Leeds will stage a 48 hour strike today.
aThe workers, members of the RMT union will also implement an on-going overtime ban, in a dispute over regrading.
RMT General Secretary Bob Crow said: "RMT firmly believe that the company has been disingenuous in their approach by failing to recognise the multi-skills and the hard work that this group of maintenance depot drivers bring to the Northern Rail operation.
"The union is clear that the job is complex and demanding, and that now is the time for the company to acknowledge that Maintenance Depot Drivers should be re-graded accordingly in recognition of their role and responsibilities."
Rail commuters in Yorkshire could face extra costs as the Government consider introducing charges at rail station car parks.
There are 18 stations in the county where parking is currently free but, under new negotiations between the Government and Northern Rail, could see charges introduced.
Currently the Government subsidises Northern Rail but as Ministers look to lower costs, the shortfall may have to be made up by customers.
Would you be happy to pay for parking at your local station? Let us know here or by emailing email@example.com
Full list of stations affected:
Burley in Wharfedale
Sandal and Agbrigg
Steeton and Silsden