Kyodo News agency said the British-flagged nuclear fuel transport ship Pacific Egret left the port in Tokai village, northeast of Tokyo today, a day after arriving with another armed ship that had waited off-shore.
Tokai is home to Japan Atomic Energy Agency, a research complex where the plutonium had been used for research.
The ship, operated by Pacific Nuclear Transport Limited, was to take the 331 kilograms of plutonium to a US government facility in South Carolina under Japan's 2014 pledge.