Central Trains has cut 10% of its services and is running replacement buses in emergency timetables changes.
There will be fewer chances to catch a train in the new year
Drivers are declining to work overtime, leaving the operator short of staff to run a full service.
Central provides the bulk of services across the Midlands and into East Anglia, the North West and Wales.
The Aslef union is balloting members, closing on 17 January, over industrial action in support of two members who have had their grading reduced.
The new timetables will run from Saturday until further notice, but will face further cuts if ASLEF members take action later in the month.
Buses are being used on many services through Lincolnshire, affecting Lincoln, Doncaster, Peterborough and Skegness.
They will also operate on some Black Country services in the Wolverhampton, Walsall, Rugeley and Stafford area.
Other lines are operating with fewer trains, although Central pledged to restrict cuts to off-peak services where possible.
On Tuesday commuters returning to work after the holiday period are expected to face disruption using timetables finalised in the last few days.
Steve Banaghan, deputy managing director of Central trains, has written to passengers.
He said: "Unfortunately we have no choice but to reduce some of our services in the current timetable so that we can be sure we will have enough drivers on duty to run the majority of our planned services.
"We aim to be able to provide you with a consistent service and avoid last minute cancellations despite the ASLEF action."
An overtime agreement covering Central Trains drivers expired on 31 December. The two sides have not reached a deal, with ASLEF now drivers now declining to work extra shifts.
Central Trains is owned by the National Express group and two other rail operators, under the same parent company, are also facing timetable problems caused by drivers working contracted hours, but refusing to work overtime.
Silverlink is facing action on its services shadowing the M1 from London to Milton Keynes and Northampton on Sunday.
And hundreds of trains were cancelled on two Sundays in 2004 on the Midland Mainline, connecting London with Bedfordshire, Northamptonshire, the East Midlands and Sheffield.