Trains on the Fife Circle were significantly disrupted after signalling cables were cut.
The fault was discovered in the early hours of the morning between Cowdenbeath and Dunfermline, where two cables were found severed.
Services are still disrupted although some have now returned to normal.
Network Rail and the British Transport Police attended the scene and an investigation into suspected vandalism of the train line is under way.
Officers from the British Transport Police were called at 06:30 to the railway tracks near Lochgelly, in Fife, following a report of damage to the signalling systems.
ScotRail confirmed services between Cowdenbeath and Dunfermline on the Fife Circle were significantly disrupted.
Work to repair the cables is underway and many services have begun operating again, although services from Glenrothes with Thornton to Edinburgh via Dunfermline Town are having to start from Inverkeithing while repairs are carried out.
ScotRail said valid tickets will be accepted on selected Stagecoach buses in Fife while affected lines are fixed.
A spokesman for Network Rail said it was first made aware of the issue at about 04:00 when signalling systems in the area failed.
He said they understood the inconvenience for passengers, adding: "The damage was significant and a section had to be cut out and replaced with new cabling.
"This has now been done and we are in the process of testing the signalling before reopening the section of track."
After an initial assessment of the site, Network Rail confirmed that two cables had been found cut and more signalling engineers were on the way to the scene.
The British Transport Police said it was investigating "exactly how much cable was damaged and who was responsible". It has asked anyone with information to contact them.