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Commuters are facing delays of up to an hour after a signalling problem at Faversham.
Southeastern have apologised for the "significant" delays to the service, mainly affecting trains between Faversham and Whitstable but also causing problems from as far away as London.
There is also reports of delays affecting services from Canterbury East and Sheerness.
Tickets are being accepted on High Speed services between Faversham and St Pancras in both directions at no additional cost.