The London Ambulance Service has said that three people were checked at the scene but did not require hospital treatment.
"There's going to be major delays when I come home too".
"There is a fault with a set of points on one of the lines approaching London Waterloo".
Commuters have been advised to use alternative routes, while also being warned that other surrounding stations are bound to be "very busy", and that queueing systems may be put in place.
"Engineers have worked overnight, however a further issue was identified and this caused delays to services using platforms 11 and 12".
Numerous trains running have been cancelled or are are stopping or starting short of the station, the rail operator said.
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She was awarded the Nobel Prize for Peace shared with child rights activist Kailash Satyarthi, in 2014. Well done to all A-level students - the hardest year.
He added: "An investigation to establish the cause of the incident is underway".
Eyewitness Vince Gannon tweeted: "Train leaving Waterloo appears to have struck a works train".
London Waterloo is undergoing three weeks improvement works to extend platforms and increase capacity, with the £800m works now scheduled to continue until August 28.
South West Trains are only reporting the incident as an "operational incident".
"Work to "re-rail" the train is under way this afternoon".
The company said: "South West Trains are advising not to travel into London at this time".
Commanding Inspector Sean McGachie said: " There were very few passengers on board and no injuries have been reported.
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