A candidate opposed to the relocation of a US naval base appears to have won an emphatic election victory in the Japanese prefecture of Okinawa, in a potential blow to Tokyo’s ties with the US, its most important ally.

On Sunday evening Takeshi Onaga seemed assured of defeating other candidates – including the two-term incumbent, Hirokazu Nakaima, who was backed by the ruling Liberal Democratic party – in the race to become the new governor of Okinawa, according to projections from Kyodo, the news agency.

Mr Onaga, a 64-year-old former mayor of Naha, the prefectural capital, fought a campaign based on his opposition to plans to relocate the base in the densely populated city of Ginowan, to a new site in the Henoko district of the city of Nago, about 30km to the northeast.

Last December, Mr Nakaima had approved a request by the central government to start filling in part of the bay in Henoko in preparation for the move, drawing outrage from anti-base protesters.

The result is likely to cause a diplomatic headache for Shinzo Abe, prime minister, who is on the cusp of a decision to call a snap election to push back an unpopular plan to raise taxes.

The long dispute over the base has embroiled both the Japanese and US national governments and local officials in Okinawa, an island prefecture which hosts about half of the nearly 40,000 US military personnel stationed in Japan.

Tokyo and Washington agreed in 1996 to move the Futenma base to the new location, not long after the rape of a local schoolgirl by a US serviceman ignited anger among local residents. Many were already unhappy about the noise and occasional accidents created by the facility.

But there was never sufficient support from local leaders to allow the deal to be implemented, as many Okinawans still want the base moved out of the prefecture altogether. Prospects for a relocation faded in 2009 when Yukio Hatoyama, then Japan’s prime minister, threw his support behind anti-base activists by saying he wanted to renegotiate the original agreement.

Mr Nakaima had said he would work to have Futenma shut within five years – a pledge that was complicated by the January 2014 re-election of a Nago mayor staunchly opposed to hosting the base.

Mr Nakaima acknowledged that financial aid promised by Mr Abe for Okinawa had played a part in his decision, as did heightened tensions between Japan and China. Okinawa administers the Senkaku Islands, the uninhabited chain at the centre of a territorial dispute with China, which calls them the Diaoyu.

Before Sunday’s election, chief cabinet secretary Yoshihide Suga had described the Futenma relocation as “an issue of the past.”

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