No trains are running out of the high-level station, which is affecting services to Edinburgh and Aberdeen.
Network Rail said a piece of machinery broke down shortly before 4am on Tuesday and they are working to remove it.
ScotRail said it was working to secure replacement buses and stressed that low-level services to Edinburgh were not affected.
A Network Rail spokesman said: “Overnight, Network Rail engineers were carrying out work to the track and overhead line equipment at Cowlais.
“Shortly before 04.00, a piece of machinery broke down. Network Rail workers are currently working to remove the failed equipment.
“Due to the nature of the incident, no trains are currently able to run from the high-level platforms at Glasgow Queen Street railway station.
“Passengers are urged to check before they travel via National Rail Enquiries or with their train operator.
“We’d like to apologise for any disruption this incident is causing and thank passengers for their patience.”
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