The blaze came just hours after a blast ripped through a warehouse at a US military post near Tokyo, sending sparks into the sky and triggering a blaze that burned through the night, although there were no reports of injuries.
Read: Explosion at chemical plant in eastern China, nine injured: state media
Local police declined to speculate on whether there was any link between the two incidents.
"We do not know any details at this point," a police spokesperson told AFP on the question of any connection.
The site near the busy international airport is owned by a unit of giant steelmaker Nippon Steel & Sumitomo Metal, which declined to make an immediate comment.
The vast steel pipe-making facility, which spans 20,800 square metres (224,000 square feet), operates a pair of manufacturing lines, about one kilometre from Haneda.
"A fire broke out from a two-metre cooling tower," the fire official said without elaborating.
Aerial television footage showed the blaze stretched across a long, narrow warehouse after it was first reported at 11:36 am local time (0236 GMT).
It reportedly spread to a next door cosmetics factory owned by Japan's Kao. Public broadcaster NHK said about 600 of its employees had been evacuated from the site.
There was no immediate word about employees working at the Nippon Steel factory or if anyone at either site was injured.
Read: Four new fires at China blast site, widespread safety hazards found
Japan Airlines and rival All Nippon Airways said none of its flights had so far been affected.
Last year, at least 15 people were injured after an explosion at a Nippon Steel plant in central Japan.
It followed a series of accidents at the site, which prompted the mayor of Tokai, a city of about 100,000 people, to formally ask the steelmaker to draw up a plan to deal with any safety problems.
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