It was not immediately clear by what margin voters had cast ballots opposing the relocation of the Futenma base from a densely-populated area to a more remote coastal region elsewhere on the southern Japanese island.

But local media including public broadcaster NHK and the Kyodo news agency said a majority of voters were in opposition to the move, which is backed by the Japanese and US governments.

Turnout in the referendum was also not immediately clear, with official figures not expected for several hours after polls closed at 8:00pm local time (1100GMT).

Okinawa's governor is required to "respect" the vote's outcome if at least a quarter of eligible voters -- around 290,000 votes -- vote for any one option.

The referendum was initially planned as a yes-no vote on the relocation plan, but a "neither" option was added after some regions opposed to the relocation threatened to boycott the poll.

Okinawa accounts for less than one percent of Japan's total land area, but hosts more than half of the approximately 47,000 American military personnel stationed in Japan.

Residents opposed to the relocation want to see the base moved elsewhere in Japan, arguing that the responsibility for hosting US troops should be spread more evenly across the country.