Two cargo ships collided south of Tokyo early on Friday, and the coast guard was searching for six missing crew from the smaller vessel.
The Japanese ship capsized after it crashed with the Sierra Leone-registered Jia Hui about 11 kilometres west of Izu Oshima Island, coast guard spokesman Yoshiyuki Terakado said.
The coast guard sent patrol boats and helicopters to search for the missing, including skipper Shingo Okawa, 62, and deputy skipper Tomokai Takai, 40.
The 12 Chinese and one Malay on the Jia Hui appear to be safe, but details are being confirmed.
The 498-tonne Eifuku Maru No. 18 was travelling from Nagoya, central Japan, to Ichikawa, east of Tokyo. The 2,962-tonne Jia Hui was headed from Kawasaki, Japan, to Busan, South Korea.