Southern Rail reported a fault with the signalling system just after 12.20pm.
This is expected until 4pm, Southern said.
A spokesperson added: "Trains can now run as normal, however there may be some ongoing delays whilst we get services affected by this disruption back to their advertised times."
The fault, which has now been fixed, was confirmed as a 'Track Circuit Failure'.
"This means the signalling system is unable to automatically verify if the next section of track past the affected signal is clear," read a statement on the Southern website.
"The rail network is designed so that if a signal stops working, trains will stop before they reach it.
"Whilst this issue is ongoing, train crew will stop at the affected signal and contact the signalling centre to confirm their location.
"At this point the signaller will verbally authorise the driver to continue towards the next signal. This process adds time to every train's journey, which means services can experience short delays."