Five people were seriously injured in the accident, which occurred just before the hydrofoil was due to arrive on Sado island after a short trip from the mainland, the Japan Coast Guard said.
It is likely the ferry hit a whale, as both humpbacks and minks are often found in the area, public broadcaster NHK quoted a marine wildlife expert as saying.
“It was a huge impact,” a passenger told NHK. “One person was bleeding.”
There was damage to the back of the vessel, local media said, but the ferry — with 121 passengers and four crew on board — reached its destination without outside help, local media said.