Network Rail said the issue was affecting Thameslink, Gatwick Express and Southern Rail trains leaving London.
Stations in London are reported to be extremely busy.
A spokesman for Network Rail Kent and Sussex has now confirmed that the signal system has been restored.
The spokesman tweeted: “Our signalling system is back online however we are not going to be able to immediately restore a full rush hour service, as trains and crew are all displaced and London Bridge and London Victoria are very, very busy.”
According to Southern Rail, trains may be delayed, cancelled, amended or diverted until the end of the day.
Customers are being ‘strongly advised’ to avoid travelling to East Croydon.
They are also being asked to avoid travelling to London Bridge, London Victoria or Gatwick Airport.
“These stations are very busy and may be closed at short notice,” a spokesman for the Southern Rail said.
Shortly before 7pm, a Network Rail spokesman said London Victoria had been temporarily closed on one side ‘owing to overcrowding’.
“Please delay your travel from Victoria this evening if you can,” the spokesman said. “Trains are running but not a normal evening rush hour service.”
More to follow.