Click here to see more photos of the fire
The blaze broke out shortly after noon (1206GMT) in an industrial area in Stratford, authorities said. The fire is within the construction site for the 2012 Summer Olympics, the British Broadcasting Corp. reported.
About 75 firefighters from 15 fire engines were fighting the blaze, the London Fire Brigade said.
Extensive redevelopment is taking place in the area, about 9 kilometers (5.5 miles) east of central London.
Police said there was nothing to suggest a suspicious cause.
"We only know it's a fire," a Metropolitan Police spokeswoman said. "There's nothing to suggest anything else at the moment."
There were no reports of injuries. One railway line was closed because of smoke, Network Rail said.
The discovery of the submarine has unveiled a few "inconsistencies." For example, how can one explain the fact that the sub was found where it needed to be searched for from the start?