Staff discovered early on Wednesday that someone had stolen the tub from a shared bathroom for men on the 10th floor of the hotel in Kamogawa, by the Pacific Ocean.
But police said they found no signs that the heavy bathtub had been dragged out of the hotel.
"The door to the room had been locked with chains, but the chains were found cut off this morning," a police spokesman said.
"We really don't know how this happened at this stage. But what we can assume now is that more than one person was involved in this incident."
A similar bathtub in the hotel's shared bathroom for women is still in place, he said.
