First Capital Connect have cancelled 28 services on London lines
A shortage of drivers has again brought disruption to trains in Hertfordshire, Cambridgeshire and Norfolk.
First Capital Connect (FCC) said it has cancelled 10 trains out of 487 on its Great Northern line but unions insist they are not taking industrial action.
The union said drivers are exercising their right not to work overtime.
FCC, also running emergency timetables on routes between Bedford and Brighton, has apologised for weekday disruption on lines between London and Norfolk.
First Capital Connect, which relies on overtime working to run its full service, said it was "extremely sorry" that a shortage of train drivers had forced the company to introduce a revised timetable on Thameslink services.
"We have introduced this timetable to allow us to operate as consistent a service as possible over the coming days
"This timetable will operate on Mondays to Fridays until further notice.
We will endeavour to operate a normal service on Saturdays and Sundays," said FCC in a statement.
Pay dispute ballot
The Great Northern route between London and Norfolk was hit by cancellations on a Sunday earlier this month but weekday disruption has been limited.
FCC anticipated 28 cancellations but have been able to reinstate some services and limit disruption to about 10 trains.
Bob Crow, general secretary of the Rail Maritime and Transport (RMT) union, said: "It is down to the company to ensure adequate staffing resources and with 2.5m unemployed, why are train services being run on what is effectively compulsory overtime?
"First Capital Connect needs to start talking seriously with the trade unions about the issues at the heart of the continuing service failure."
The company has held talks with the drivers' union Aslef and is planning further discussions.
Aslef said it is balloting members for industrial action over a two-year pay offer which would mean at least 3% from next April.