Plans to relocate a US marine corps airbase on Okinawa in southern Japan have been thrown into doubt after an anti-base candidate won the race to become the island’s governor.

Takeshi Onaga is set to easily defeat his main rival, the pro-relocation incumbent Hirokazu Nakaima, according to exit polls cited by Japanese media.

Onaga’s victory poses a headache for Japan’s prime minister, Shinzo Abe, who supports the transfer of Futenma base from the middle of a densely populated city to a remote site off Okinawa’s north-east coast.

The result will also cause concern in Washington, which has been pushing for construction of the new base since the mid-1990s. Pentagon officials say the relocation is vital to the region’s security given rising tensions with China and North Korea’s nuclear weapons programme.

Onaga told supporters he would “act with determination” to withdraw permission to conduct landfill work at the site of the proposed base, a move that would effectively halt construction.

The Futenma move has long been a thorn in the side of US-Japan security ties. Tokyo and Washington agreed to the move after the 1995 rape of a 12-year-old girl in Okinawa by three US servicemen sparked mass demonstrations and calls for Washington to reduce its military footprint on the island.

In a concession to residents, the US also agreed to transfer about 8,000 troops and their families to Guam and Hawaii.

Yet almost two decades on, local opposition to the move and political indecision in Tokyo means not a single marine or piece of military hardware has been moved.

Okinawa, about 1,000 miles south of Tokyo, hosts more than half of the 47,000 US troops in Japan and three-quarters of US bases.

Many Okinawans, angered by pollution, crimes involving servicemen and the risk of aircraft accidents, are demanding that Futenma be moved off the island altogether.

Opponents of the US military presence say the proposed replacement for Futenma, a V-shaped runway built on reclaimed land, would threaten the safety of local residents and destroy the area’s marine ecosystem.

Abe received a boost last December when Nakaima, who had opposed the relocation, unexpectedly gave his approval for drilling surveys to begin at the site.

Nakaima, who was backed by Abe’s Liberal Democratic party in Sunday’s election, sparked anger among many Okinawans who accused him of being bribed by central government promises of massive investment in the prefecture, the poorest in Japan.

“We proved that the people of Okinawa disagree [with Nakaima],” Onaga, a former mayor of the Okinawan capital, Naha, was quoted as saying by Kyodo. Describing the result as “a new page in history”, he added: “I am determined to work towards cancelling and withdrawing” permission for construction.