The firm has seen a marked decline in its performance in the last week, with Tuesday seeing 38.8 per cent of its trains at least 30 minutes late or not running at all and a further 23.7 per cent between 10 and 30 minutes late.
The following day, 24.2 per cent of trains were cancelled or very late, with 19.9 per cent on Monday and 16.1 on Sunday.
Passengers have spoken at their anger at the frequent disruption, including those on Wednesday night told that services south from Newcastle would be cancelled and that they would not be able to get on other operators' trains.
A spokeswoman for TransPennine Express said: “In the last few days, our services have been disrupted by a number of things outside of our control, mainly infrastructure incidents (such as signalling and points failures) and issues experienced by other operators.
"These external factors have accounted for 80 per cent of the issues we experienced.
“We apologise to any customers affected by this and want to assure them that we are working with Network Rail and other rail operators to deliver a more punctual and reliable service.”
The 20 per cent relating specifically to TransPennine Express are understood to include problems such as door faults and other maintenance problems caused by the firm not being able to get its trains to the depot.