The boat was carrying 121 passengers during the collision, injuring 87 people traveling on the vessel, according to the Coast Guard from the Niigata prefecture.
Five passengers had to be airlifted to hospital but they remained conscious. The crew of the high-speed vessel told officials that "it hit the object [which appeared] to be a marine creature."
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The Coast Guard dispatched vessels and helicopters to investigate the cause of the collision, but they have yet to find the alleged animal or any other cause of the crash.
The incident occurred between Niigata and Sado Island, off Japan's northwest coast.