The Panamanian-flagged Beagle III, a 12,630-ton vessel carrying steel coil, sank after colliding with the South Korean-registered Pegasus Prime in the Uraga waterway. The accident happened at about 3:10 am (1810 GMT Monday).
Of the 20 Chinese crew aboard Beagle III, "twelve have been rescued, but one of them is in a state of cardio-respiratory arrest," said a coastguard official, adding that eight others were still missing.
Rescue personnel in Japan frequently use the term cardio-respiratory arrest before doctors officially pronounce death.
The crew on the 7,406-ton Pegasus Prime, six South Koreans and eight people from Myanmar were mostly unhurt, but two Koreans sustained minor injuries when they tried to lower a lifeboat, the Japanese official said.
The sea was not believed to be rough at the time of the collision, according to the coastguard.