Lines have been blocked between Norwood Junction and London Bridge after the hole was spotted near Forest Hill.
The hole is the second to be discovered in the area in as many weeks.
A spokesman for Network Rail said: “Our engineers have been monitoring the site of the previous hole under the railway at Forest Hill since that incident occurred in mid-July.
“We spotted a small hole at 3am today and closed the two lines above it to trains.
“This new hole is about just over half a metre deep and we are working to open it out to investigate the scale of repairs we need to make today.
“Our aim is to get the railway open to trains today, however we won’t know for certain until we have completed our investigations.
“We offer our apologies to passengers traveling to London through the area this morning as their journeys will be disrupted. Please check before you travel using National Rail Enquiries or with your operator.”
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