The sardines and some mackerel washed ashore in Hakodate on Japan's northernmost main island of Hokkaido on Thursday morning, creating a silver blanket along a stretch of beach about a kilometre long.
Local residents said they have never seen anything like it.
Some gathered the fish to sell or eat.
The town, in a notice posted on its website, urged residents not to consume the fish.
Takashi Fujioka, a Hakodate Fisheries Research Institute researcher, said he has heard of similar phenomena before but it was his first time to see it.
He said the fish may have been chased by larger fish, become exhausted due to a lack of oxygen while moving in a densely packed school and were washed up by the waves.
The fish also may have suddenly entered cold waters during their migration, he said.
The decomposing fish could lower oxygen levels in the water and affect the marine environment, he said.
"We don't know for sure under what circumstances these fish were washed up, so I do not recommend" eating them, Fujioka said.
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