There was damage to the back of the vessel, local media said.
Five of the injuries were serious and a 15cm crack was found at the ferry's stern.
According to the local media, the boat was carrying 121 passengers from the Nagata port of Honshu.
Ferry operator Sado Steam Ship Co. said in a statement that the jetfoil ferry reached its destination despite the incident and apologized to the customers, saying the ship was hit by "marine life".
Public broadcaster NHK quoted a marine expert who said the scale of the impact suggests the ship hita whale. "People around me were moaning", another traveler told reporters, according to the Japan Times.
A ferry in Japan got into an accident, injuring 80 passengers.
It is though mink and humpback whales are now migrating through the Sea of Japan.
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 collision.