The 45-year-old was among 10 North Korean "fishermen" spotted aboard a tiny wooden boat struggling in bad weather off the northern island of Hokkaido in late November.
Some of them admitted to "taking out" some electronic products from a remote Japanese island where they landed briefly to take refuge.
The captain and two other crew members, who all identified themselves as North Korean nationals, were arrested earlier this month on suspicion of stealing a power generator on the small island.
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According to the indictment, the captain took the lead in stealing some 40 items ranging from home appliances to solar panels worth 5.65 million yen ($50,000), public broadcaster NHK said, adding that he will stand trial in a Japanese court.
The remaining nine crew members are all expected to be deported back to North Korea, NHK said. Prosecutors declined immediate comment when they were contacted.
Dozens of North Korean fishing vessels wash up on Japan's coast every year, but Japanese coastguards registered 28 cases last month, the highest figure since records began in 2014.
Experts say some North Korean fishermen are travelling far out to sea to satisfy government mandates for bigger catches.
But their old and poorly equipped vessels are prone to mechanical and other problems, including running out of fuel, and there are few ways for them to call for rescue.
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