The collision, between the South Korean-registered vessel, the Orchid Pia, and a Panama-registered cargo ship, occurred 13 kilometers (8 miles) off Izu Oshima Island to the south of Tokyo at 2:15 a.m. on Tuesday (17:15 GMT Monday), a spokesman for the 3rd regional maritime safety headquarters in Yokohama said.
The Panama-registered Cygnus Ace was undamaged in the collision, however, the Orchid Pia, which had a crew of seven South Koreans and nine Indonesians, disappeared from radar screens shortly after the incident and is believed to have sunk, the spokesman said.
Patrol boats and aircraft are involved in the rescue operation to try and trace the vessel and crew, South Korea's Yonhap news agency said.
So far Japan's coast guard has only recovered life vests and an emergency raft from the collision site, Yonhap said.