The vast steel pipe-making facility, which spans 20,800 square meters, operates a pair of manufacturing lines, about one kilometer from Haneda.
"A fire broke out from a two-meter 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.
It reportedly spread to a cosmetics factory owned by Japanese firm's Kao and 600 of its employees were evacuated from the site, according to NHK.
There was no immediate word about employees working at the Nippon Steel factory or if anyone at either site was injured.
Japan Airlines and rival All Nippon Airways said none of its flights had so far been affected.
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.
