South West Trains is warning of severe disruption across the whole network for the rest of the day.
The train company is advising passengers not to travel towards London Waterloo until after 09:00 after a loss of all signalling in the Earlsfield area of south-west London.
It said trains could be cancelled, delayed by up to 90 minutes or revised until the end of service.
Waterloo handles about 100 million passenger journeys a year.
SWT had already warned of disruption because of a track defect on a set of points between Woking and Surbiton, which blocked the London-bound fast line.
A Network Rail spokesman said: “Owing to a major signalling failure overnight, mainline services through Clapham Junction to Waterloo will be delayed or cancelled this morning.
“We’re sorry for the disruption this will cause to people’s journeys this morning, and will continue to work to resume a normal service as quickly as possible.”
South West Trains passengers are set to face severe disruption next month when work begins to extend platforms at Waterloo, meaning many services will not be running and some commuter stations will be closed altogether.
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