The transport ministry says a Japan-linked vessel sustained minor damage while it was anchored in the Gulf of Oman, near the Strait of Hormuz.
The ministry on Friday said no injuries were reported and no Japanese nationals were onboard.
Transport Minister Kaneko Yasushi says the incident happened on Wednesday morning Japan time. The vessel appears to have been hit by an unidentified airborne object less than 1-meter in diameter.
"We called on the Japanese Shipowners' Association to do its utmost to secure the safety of Japan-related vessels and their crews navigating in the area," the minister said.
A crewmember was cited as saying the object apparently cracked a glass window and dented an exhaust chimney. The vessel is expected to move to safer waters.
A total of 44 Japan-related vessels with a combined 24 Japanese crewmembers are in the Persian Gulf as the conflict continues in Iran. Four other vessels are in the nearby Gulf of Oman.