Tens of thousands of protesters in Okinawa vowed to stop the planned relocation of a US military base, saying they want it off the southern Japanese island entirely.

Opponents of the relocation say the plan to move US Marine Corps Air Station Futenma from a crowded neighbourhood to a less populated coastal site would not only be an environmental debacle but also ignore local wishes to remove the base.

About 70,000 people gathered at a park in the state capital of Naha under pouring rain ahead of an approaching typhoon and observed a moment of silence for Okinawa's Governor, Takeshi Onaga, who died Wednesday of cancer.

Onaga, elected in 2014, had spearheaded opposition to the relocation and criticised the central Government for ignoring the voices of Okinawans. He had filed lawsuits against the central Government and said he planned to revoke a landfill permit issued by his predecessor that is needed for construction of the new base.

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Deputy Governor Kiichiro Jahana, representing Onaga at the rally, said he will follow through with the revocation process as instructed by the Governor and succeed his "strong determination and passion".

Okinawans are trying to block the Government plan to start dumping soil into Henoko Bay within days to make a landfill for the new site of the Futenma base. Environmental groups say construction at the bay risks corals and endangered dugongs.

About half of the 50,000 US troops in Japan are on Okinawa.

- AP