The race to elect the mayor of Nago City -- where the US Marines' Futenma Air Station is set to be relocated -- pits incumbent and anti-base Susumu Inamine against Bunshin Suematsu, who supports the move.
Last month, more than 17 years after Washington and Tokyo agreed to move the base from a densely populated urban area on the island, the Okinawa government finally consented to a landfill that will enable new facilities to be built on the city's coast.
Previous polls suggest Inamine, 68, who is seeking a second four-year term as Nago's mayor, has a small lead over Suematsu, 65, a former Okinawan prefectural assembly member.
The election is being closely watched by Japan and the United States amid concerns an Inamine victory could further postpone the relocation of the Futenma base.
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The mayor of Nago does not have the right to overthrow plans to relocate the base but could refuse to approve the use of roads and other facilities in the city necessary for building works.
Okinawa's Governor Hirokazu Nakaima, long a thorn in the central government's side, gave the plan his approval after Japanese Prime Minister Shinzo Abe pledged a big cash injection into the island's economy every year until 2021.
Environmentalists say any development as a result of the relocation risks seriously damaging the coral reefs in the area as well as the delicate habitat of the dugong, a rare sea mammal.
The ballot is due to close at 8:00 pm (1100 GMT) and results are expected to come out late today.