The fault affects all services heading to Haymarket, where the problem is located, and is expected to continue to cause issues until this afternoon.
There have already been cancellations to some Fife services this morning, with all trains on the route subject to delay or revision.
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Replacement bus services are available on some routes.
ScotRail say Network Rail are already working on the problem and hope to have it fixed this afternoon.
A ScotRail spokesperson said: “We are sorry to customers for the disruption to their journey, which has been caused by a signalling fault.
“Network Rail engineers are working hard to fix the fault and we are doing everything we can to keep people moving.
“Replacement buses have been put in place at stations throughout the affected routes and we have also secured ticket acceptance wherever possible, including Edinburgh trams and Lothian buses.
“Customers are asked to check @ScotRail on Twitter or the ScotRail app for the most up to date information.”
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