The Japanese government Tuesday overturned a move by Okinawa's governor to stop work on a US base relocation site, marking the latest fight in a long-running battle over the controversial project.

The proposal to move the Futenma air base, first mooted in 1996, has become the focus of anger among locals, who insist it should be shut and a replacement built elsewhere in Japan or overseas.

Earlier this month, outspoken Okinawa governor Takeshi Onaga revoked approval for work on the base in Japan's southernmost island chain.

"We have decided to nullify (Okinawa's) cancellation of the approval," land and infrastructure minister Keiichi Ishii said after a cabinet meeting Tuesday.

Also Tuesday, top government spokesman Yoshihide Suga said Onaga's decision to halt the project was without merit.

"The national government has made the best decision it could to remove the danger associated with Futenma air base and to bring about its closure," Suga told a regular press briefing.

Tokyo's decision means that efforts to move the base from a residential area to the secluded Henoko district would press on.

Both Tokyo and Washington have repeatedly backed the plan, with Prime Minister Shinzo Abe insisting it was "the only solution".

The latest chapter was sure to inflame tensions between Tokyo and Okinawa, which reluctantly hosts more than half of the 47,000 American military personnel stationed in Japan.

Residents have bitterly complained that the rest of Japan must share the burden of hosting US military facilities, along with accidents and crimes committed by US service members.

Japanese media have reported that Okinawan officials are considering legal action to halt the project.

Work in Henoko is only in the initial stages with crews setting up sea floats and a makeshift bridge necessary for landfill work.

There is widespread agreement that Futenma's current site -- in the middle of a crowded urban area where US aircraft are a nuisance to thousands of locals -- is not appropriate.

The US says it will not close the Futenma until a replacement facility is ready.

Opponents say the existing plan to move it to Henoko, with untouched nature, would seriously damage nearby coral reefs and the delicate habitat of the dugong, a rare sea mammal.

"This decision is an insult to the people who have worked so hard, for so long, to have their voices heard," said Greenpeace Japan oceans campaigner Kazue Komatsubara.

"It is shocking that the government is failing to protect Japan's endangered species and trampling over the wishes of so many Okinawans."