The hole was discovered near Forest Hill between East Croydon and London Bridge.
Train services running to and from these stations may be cancelled, diverted or delayed by up to 40 minutes, Southern Rail has said.
The disruption is expected to last until the end of the day.
A Network Rail spokesperson said: “Earlier today a hole believed to be four metres deep was found in the Forest Hill area.
“More than 50 tonnes of ballast, which supports the track, is on its way to site to fill the hole and engineers will be working through the evening and throughout the night to try and fix the problem.
“There will be a reduced service this evening from London Bridge as people head home and we would encourage people to seek alternative routes if possible.
“Our aim is to have the railway fixed for tomorrow morning but holes like this can be unpredictable. Until the ballast is packed into the hole we won’t know for certain if the hole is stable or not so passengers are advised to check before they travel.”
“Southeastern passengers are not affected by this incident.”
Alterations to services
Southern Rail has said the following services have been amended due to the incident:
-Those travelling from Uckfield can still catch their trains from London Bridge but some will be cancelled and trains that do run may be delayed.
- Customers for Tattenham Corner and Caterham can also use trains from London Bridge but these may also be delayed.
- People travelling to Gatwick Airport should plan to travel from London Blackfriars or London Victoria
- London Bridge to Horsham services will be diverted to run between East Croydon and London Victoria and will not call at New Cross Gate or London Bridge.
- London Bridge to Caterham services will be diverted between Norwood Junction and London Bridge.
- London Bridge to Tattenham Corner services will be diverted between Norwood Junction and London Bridge
- London Victoria to London Bridge services are diverted after Streatham Hill calling at all stations via Tulse Hill to London Bridge.-
- London Bridge to Uckfield services will be diverted between Norwood Junction and London Bridge.
- London Overground services West Croydon/Crystal Palace to Dalston Junction will only run between New Cross Gate and Dalston Junction.
-London Bridge to Brighton (Thameslink services) will only run between Gatwick Airport and Brighton
For a full list visit the Southern Rail website.
Earlier delays on the line
This morning lines were blocked between Horsham and Barnham after engineering works were ‘not completed’.
Southern said: “A Network Rail engineering train developed a fault earlier today near Arundel. As a result, planned engineering works could not be completed on time and both lines between Horsham and Barnham were closed whilst the works are completed.”
All lines have now reopened but trains are running at a reduced speed between the stations.