The 80-year-old Tokyo market is known for its daily tuna auctions, which supply many of the capital's top sushi restaurants.
Smoke could be seen billowing from the market as dozens of fire engines tackled the flames on Thursday.
There are no reports of serious injuries at this stage.
The fire broke out at about 16:50 local time (07:50 GMT), Japanese broadcaster NHK said, in the outer region of the market and close to the surrounding area's narrow streets.
The area is home to many sushi restaurants and shops, some of which have been evacuated, NHK reports.