The Black Hawk helicopter of the Air Self-Defence Force disappeared from radar at around 6:00 pm (0900 GMT), some 31 kilometres (19 miles) south of Hamamatsu, a ministry spokesperson said.
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Some parts suspected to have belonged to the rescue chopper were found floating around the area, the spokesperson said, adding: "We are searching for the four crew members."
Quoting a government source, Kyodo News said the helicopter, which was conducting a night time search-and-rescue drill, was likely to have crashed.
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