Network Rail said a 30cm hole was found beneath the railway lines near Forest Hill at 3am.
Lines have been blocked between Norwood Junction and London Bridge and services are expected to be cancelled and delayed throughout the evening.
A spokesman for Govia Thameslink Railway (GTR) said: “This means that capacity into London Bridge is severely reduced while Network Rail works to make repairs, with many services diverted, starting/terminating short of their destinations or cancelled. These alterations will remain in place until the end of service today.
“Passengers are advised to use either Victoria or Blackfriars tonight. Southern tickets are being accepted on London Buses, London Underground, Southeastern and Tramlink between Beckenham Junction and Croydon.”
Robert Coulson, acting director for Network Rail, said: “Our engineers are continuing to work at the site of the hole at Forest Hill but we are now expecting disruption to trains for the rest of today.
“I’m really sorry that passengers have had to put up with this disruption today and I know that people are upset and will want to know we are doing everything we can to return their railway to them.”
Southern services travelling towards London Bridge are unable to call at Norwood Junction, Anerley, Penge West, Sydenham, Forest Hill, Honor Oak Park, Brockley, and New Cross Gate, GTR has said.
“Customers for these stations will need to travel to London Bridge first and change there for services to these locations. Trains towards London Bridge may be diverted via Tulse Hill to avoid the affected line, which will add up to 20 minutes to your journey time. Some cancellations are also expected between Purley and Caterham, a spokesman said.
“Uckfield and East Grinstead services will run as normal from London Bridge but may experience delays.
“Thameslink services that run between London Bridge and Brighton are running between Gatwick Airport and Brighton only. Thameslink services are running normally between Brighton and Bedford.
“London Overground services are unable to run between New Cross Gate and Crystal Palace / West Croydon
“Disruption is expected to continue until end of service.
“Passengers are advised to check before they travel at www.nationalrail.co.uk.”
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