A Network Rail statement said: "South West Trains and Network Rail are advising passengers not to travel following a low-speed, partial derailment at London Waterloo this morning".
South West Trains said passengers should expect limited services running to and from Waterloo as it was dealing with an "operational incident". Some services will start or end before London Waterloo.
Trains are unable to use platforms 1 to 13 at London Waterloo, while platforms 1 to 10 were already out of use because of the ongoing improvement works.
At 5.40am on Tuesday a passenger train collided with a stationary barrier train.More news: No reason why more games won't come out on Switch
A South West train is believed to have hit a freight train and left the rails on one side. Most trains are experiencing severe delays and are subject to short notice alterations.
"In addition, South West Trains are investigating a problem near Waterloo station, which is expected to cause some further delay".
"Upgrade work to extend platforms at Waterloo continues".
Inquiries are under way to establish why the accident there and another at King's Cross happened, the British Transport Police and Network Rail said.More news: Gene editing may pave way for pig to human organ transplants
Passengers are being advised to use alternative routes and have been warned other stations in the area will be "very busy" with the possibility of queuing systems being put in place.
Trains travelling from Weymouth are due to terminate at Basingstoke.
When this happens, trains have to wait for platforms to become free, occupying the track outside Waterloo and making it more hard to get trains moving.More news: Monday continues the great weather with more sunshine and low humidity