Typhoon Nangka made landfall in southwestern Japan on the night of July 16 and slowly moved northward before turning into a tropical depression.
Torrential rain and gusts of wind wreaked havoc in various parts of western Japan, also causing high waves and clouding sea water in the fish farm near the Pacific coastal town of Kushimoto, Kyodo News and the Asahi newspaper reported.
The storm caused the sensitive bluefin tuna to panic, the Asahi said, with the Mainichi daily saying the waves had driven many of them into a barrier.
A local government official was not immediately available at weekend.
Bluefin is usually the most expensive fish available at Tokyo's Tsukiji, the biggest fish and wholesale seafood market in the world, with a 180-kilogramme (380 pound) wild tuna auctioned for 4.51 million yen (USD 36,400) in January.
But environmentalists warn that the surging global popularity for the fish is placing "unsustainable pressure" on the species, increasing the demand for farmed tuna in Japan.
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