The eight men were arrested earlier this year and face charges of violating Japan's Stimulant Drugs Control Law, the Tokyo District Prosecutors' office said in a statement.
The Turubong 1 ship was allegedly carrying 237 kilograms (522 pounds) of amphetamines from Chongjin, a North Korean port, in November 2002 to a prearranged point in the Sea of Japan, the statement said.
The ship dropped off the cargo for pickup by a Japanese vessel owned by one of the arrested men, but the vessel failed to find the cargo due to bad weather, according to the statement. Japanese police later discovered the drugs washed ashore on the country's northwestern coast.
The boat was seized and searched by Japanese authorities in May, and later returned to North Korea, according to the AP.
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