Dozens of Nomura's jellyfish sunk the Diasan Shinsho-maru boat and sent its three-man crew into the sea, The Mainichi Daily News reported.
The organisms can weigh up to 440lbs and grow up to 6ft in diameter.
The three men forced into the sea, near Chosi, were rescued by another trawler.
Waters around Japan have been inundated with the jellyfish this year.
Experts believe weather and water conditions in the breeding grounds off the coast of China have been ideal for the species in recent months.
"The arrival is inevitable," Hiroshima University Professor Shinichi Ue told the Yomiuri newspaper.
Echizen kurage, or Nomura's jellyfish, are caught in a fishing net off the shores of Awashimaura, northern Japan, in 2003
"A huge jellyfish typhoon will hit the country."
Nomura's jellyfish have been known to wreak havoc in Japanese waters.
They destroy fishing nets, poison fish in the nets and render them unfit for sale, sting humans and even disable nuclear power stations by blocking pumps used to cool the reactors.
In 2007, there were 15,500 reports of damage caused to fishing equipment by jellyfish in the region, The Daily Telegraph reported.
Many fishermen have tried to keep jellyfish out of their nets by using sharp wires.
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