The H-60 helicopter made a hard landing on the Navy cargo vessel USNS Red Cloud around 30 kilometers east of Okinawa, US Forces Japan said in a statement, adding that the cause of the incident was under investigation.
Okinawa is home to most of the tens of thousands of US troops in Japan.
The injured were transported to a Navy hospital, the statement said. Their conditions were not immediately clear. The other 10 people aboard the helicopter were not hurt, said Japanese coast guard spokesman Shinya Terada.
The presence of thousands of US troops on Okinawa, where more than half of about 50,000 American troops in Japan are concentrated, has been a source of friction.
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A plan formulated in 1996 between the Japanese and American governments would move U.S. Marine Air Station Futenma from a populated neighborhood to a less developed area, but Okinawans worried about safety, crime and noise want the base moved off the island altogether.
Today's accident coincided with Japanese Chief Cabinet Secretary Yoshihide Suga's visit to the island for talks with Okinawa Gov Takeshi Onaga, a vocal opponent of the relocation plan.