The closure of two platforms at Waterloo is expected to cause delays for rush hour commuters travelling from the station for the rest of the evening.
A signalling problem has resulted in the closure of platforms three and four, resulting in delays as well as disruptions to normal routes.
South West Trains which runs services to and from the station said platforms 20 and 21 have been opened to help minimise the delays.
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Commuters can expect changes to train platforms in addition to cancellations and some services not stopping at the usual stations.
"Engineers have investigated the issue and due to the nature of the fault can only rectify the problem after the last trains have departed London Waterloo," said National Rail.
It's the second time this week passengers on the route have been hit beset by disruption after an incident at Raynes Park caused chaos on Tuesday.