A new timetable was introduced on Thursday, but due to problems with the new fleet of trains and a shortage of trained drivers many services have been cancelled.
TransPennine Express will run a reduced service until January 5.
Leo Goodwin, managing director for TransPennine Express said: “I am truly sorry for the continued disruption to journeys this week.
"I know what a busy time it is with everyone juggling work, visiting loved ones or trying to go out and enjoy the party season.
"As we bring in our new trains, it has had an associated impact upon our training schedule and our train maintenance plan which is having a big knock-on effect to our services."
Full list of cancellations from Saturday afternoon
14:10 Manchester Airport to Newcastle due 17:13
14:24 Liverpool Lime Street to Edinburgh due 18:56
14:54 Liverpool Lime Street to Scarborough due 17:51
15:10 Manchester Airport to Newcastle due 18:10
15:54 Liverpool Lime Street to Scarborough due 18:52
16:21 Edinburgh to Liverpool Lime Street due 20:56
16:24 Liverpool Lime Street to Edinburgh due 20:54
16:30 Manchester Piccadilly to Hull due 18:37
17:43 Newcastle to Manchester Airport due 20:40
18:33 Edinburgh to Liverpool Lime Street due 23:06
18:34 Scarborough to Manchester Victoria due 20:52
18:43 Newcastle to Manchester Victoria due 21:11
19:08 Hull to Manchester Piccadilly due 21:04
19:30 Edinburgh to Liverpool Lime Street due 00:05
19:34 Scarborough to Manchester Airport due 22:22
21:08 Liverpool Lime Street to Newcastle due 00:14
21:35 Manchester Airport to York due 23:40
22:15 Scarborough to Manchester Airport due 00:49