Travellers have been advised to avoid London Waterloo until Thursday after a train derailed outside the station.
The train partly left the tracks as it was pulling away from a platform at low speed at 05:40 BST, Network Rail said.
Three people were checked over by London Ambulance Service but nobody was taken to hospital.
Trains are unable to access 13 of the station's 24 platforms as 10 were already closed owing to engineering works to enlarge its capacity.
Public transport in London was further disrupted when a passenger train crashed into buffers at King's Cross station and Holborn Tube station was evacuated because of a fire alert.
Emergency services including police, paramedics and fire crews were called to Waterloo.
Insp Sean McGachie of British Transport Police (BTP) said "very few passengers had been on board" and officers were "working with industry partners to investigate the circumstances".
The passenger train was carrying 23 passengers and two staff members when it crashed into a "barrier train" which had been in place to separate engineering works from operational trains, according to Network Rail.
Chris Denham, a spokesman for Network Rail, told the BBC the partially derailed train had blocked three of the platforms so only very limited services could run.
"If you don't have to travel to Waterloo today, please don't," he said.
South West Trains said there would be a very limited service running to and from Waterloo until Thursday and have advised travellers not to use their entire network.
Many of the trains running have been cancelled or are stopping or starting short of the station, the rail operator said.
Passengers have been warned other stations in the area will also be "very busy".
Some stations including Waterloo, Vauxhall, Clapham Junction and Wimbledon all have queuing systems in place to manage the number of people on platforms.
The ongoing £800m engineering project at Waterloo will prepare the station for longer trains and provide space for 30% extra passengers during the busiest times of the day.
The station is usually one of the busiest in the UK, with an average of 270,000 journeys made to and from it each day.
In north London, a Great Northern train hit the buffers at King's Cross station at 06:20.
Natasha Coella, who had boarded the train at Stevenage, said passengers "went flying" as the train arrived at the station.
"No-one expected it and people just went from one end of the carriage to the other," she said.
A spokesperson for the rail company said it had happened at low speed and the Rail Accident Investigation Branch had been informed.
In a separate incident, Holborn Tube station was evacuated for a short period after reports that smoke had filled carriages on a Central line train.
BTP said the problem had been caused by a defective train.