A spokesperson for Transport for London said: "The driver, following London Underground's stringent safety procedures, stopped the train immediately, and our signalling system prevented any eastbound trains from moving towards the stationary train.
"The nearest eastbound train was stationary at red signals almost a kilometre away at West Ham.
"Passenger and staff safety was maintained throughout. The train had three passengers on board, who were all removed from it shortly after 9am. Our engineers are carrying out a full investigation into the cause of this signalling irregularity, and the Rail Accident Investigation Branch and the Office of Rail Regulation have been informed of the incident."
The BBC report that services on the line were suspended for about six hours to allow investigations to take place. Initial findings seem to have have identified a fault with signalling equipment at Plaistow station.
At time of writing there's been no statement from RMT union leader Bob Crow on this. After the runaway train on the Northern Line he was quick to use the incident to his advantage and said "This horrific failure comes against a background of a systematic reduction in safety-critical jobs and safety procedures as a direct result of TfL's financial cuts programme."