The Tsukiji fish market is the biggest in the world and a major tourist draw for the Japanese capital.
The fire damaged roughly 935 sq. meters of the three-story building, which started at around 4:50 p.m. Thursday. The broadcaster also said the fire broke out outside of the market and close to the surrounding streets.
Everyone in the area was evacuated to safety and there were no reports of injuries related to the fire, although one firefighter fell ill, possibly from smoke inhalation or heat exhaustion, local media reported.
Some 60 fire trucks were dispatched to the market to control the flames which originated inside an area with small shops hard to access, reports Efe news.More news: AA sacks boss for 'gross misconduct
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Tsukiji's interior industrial market - where the famous tuna auctions take place - was undamaged and the area was open to tourists as usual. Reports say the flames affected mostly wooden buildings in the market.
The market, which was built back in 1935, has supplied many restaurants in the city for years.
More than 1,600 tonnes of seafood worth some 1.6 billion yen (S$19.7 million) pass through the market every day.
Tokyo's governor, Yuriko Koike, has previously said the market needs to be rebuilt because of its age - and the associated risk of it being vulnerable to earthquakes, which are not uncommon in Japan. The relocation will reportedly happen later this year.