Smoke from the fire could be seen across London
Aerial footage
More than 75 firefighters tackled the blaze as 50ft (15m) flames engulfed the building in Waterden Road, Hackney Wick at about 1200 GMT on Monday.
Black smoke could be seen across the skyline and the Fire Brigade received more than 150 calls from the public.
Rail services were suspended between Dalston Kingsland and Stratford but roads in the area remained open.
The warehouse is on the western edge of the proposed site of the Olympic Village and was due to be demolished on Monday.
Assistant Commissioner Dave Brown, of the London Fire Brigade, said investigations were ongoing but the fire was not thought to be suspicious.
Health risks
He also confirmed that asbestos had been found on the site.
Professor Virginia Murray, of the Health Protection Agency, sought to reassure people over the substance.
She said that research showed it was usually long-term exposure to asbestos which causes a significant health risk.
The blaze has disrupted rail services in east London
Your pictures of the fire
"Our advice is not to touch any of the material that may have come from the fire and make sure that they (members of the public) get in touch with their local authority so that an appropriate clean-up can be undertaken," she said.
The Olympic Delivery Authority (ODA) Chief Executive David Higgins said it would carry out a full investigation into the fire.
He said: "Initial indications would suggest that this was an accident rather than arson.
"We are in touch with local residents and are keeping them informed of the situation."
He said that work was continuing in the rest of the park.
Transport disrupted
The blaze was close to the Channel Tunnel high speed rail link but Eurostar said the fire did not have an impact on services.
Flights from nearby London City Airport were also unaffected by the fire.
A Transport for London spokesman said services on the overground line from Richmond were terminating at Dalston Kingsland.
Fire crews were expected to remain at the site overnight to ensure the fire is damped down properly.
City of London, approximately 5.5 km (3.4 miles) from the fire. 
A huge fire was reported in Hackney Wick eastern London, England, on part of the 2012 Olympic Games site scheduled to be the location of the handball courts.

Flames are visible from Canary Wharf and the smoke plume is visible across the whole of the City of London. The fire, at a disused single-storey warehouse in Waterden Road, Stratford, is said to have been reported around 12:05 GMT. The Associated Press reports say that a "large explosion" preceded the fire; eyewitnesses do not confirm this, though there is flammable material on the site.  David Jones of East London Bus company states that the fire started at a disused warehouse adjacent to their Waterden Road depot.

Eight fire appliances and 40 fire-fighters were initially deployed. The winds carried the smoke over London and reports suggested that the plume of smoke was visible from Rochester, Kent.

By 13:15 GMT the London Fire Brigade reported that there were 15 appliances and around 75 firefighters, and the fire was not yet under control.

Police say they have no evidence of a terrorist attack at this time.

Charles Buchanan of London City Airport told BBC News that the airport was still operational but had closed one runway whose flight path crosses the smoke plume, though services are unaffected.  A short stretch of railway close to Hackney Wick was temporarily closed but suffered no damage.

London Ambulance Service confirms that there are no known casualties and their emergency response team has been stood down, though their hazardous area team remains on site. Police are holding back large crowds of bystanders.