The issue at Hamilton Central station led to services in the direction of Larkhall and Motherwell being cancelled.
Engineers from Network Rail are on the scene but disruption is expected to continue until 2pm today.
The main line from Edinburgh to Glasgow is unaffected.
Dozens of ScotRail services have been cancelled each day in recent weeks, many because of staff training for new services.
This has yet to be completed despite the launch of an expanded timetable ten days ago because two fleets of trains have arrived late.
Politicians vented their anger at the disruption, with Ettrick, Roxburgh and Berwickshire Conservative Rachael Hamilton describing the impact on the Borders Railway as “absolutely unacceptable”.
Edinburgh Western Liberal Democrat Alex Cole-Hamilton said Edinburgh-bound commuters in Dalmeny had been unable to board trains they were so full.
Transport secretary Michael Matheson said he was “extremely disappointed” to be still speaking about the level of cancelled trains.