TransPennine Express said it is reducing its level of service across all routes to "provide a greater level of certainty for customers" as it attempts to manage an increasing number of absent and sick staff.
It said coronavirus, "increased levels of sickness", and the Omicron variant, as well as some industrial relations issues have caused the disruption.
The amended timetable will be implemented from Monday January 10.
Last month, passengers in Scarborough reported a number of cancellations in the run-up to Christmas Day, with hours of delays before the next available train.
The disruption comes just a month after the company reintroduced hourly services to York and Manchester, with staff now struggling to operate to schedule.
Matthew Golton, Managing Director for TransPennine Express said: "While we are disappointed to be making these changes and reducing services, our priority is keeping people moving and providing a greater level of certainty for our customers.
"We are sorry for any disruption this may cause to journeys and call on our customers to allow additional time for travel and to check carefully – for any changes to train times.
"We will continue to regularly review these changes in line with the current situation."
Passengers are advised to allow for extra time and to check before they travel. TransPennine Express said services on weekends may be different due to engineering works taking place.
For more information on the disruption and services changes, visit the TransPennine Express website here.