The plan to relocate Futenma air base to the Henoko region, 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.
Outspoken governor Takeshi Onaga said his government has began procedures to cancel approval, just two days after work in Henoko resumed following a month-long delay, according to the prefecture.
"We'll do our best by using every possible measure to block the construction of a new base in Henoko as promised during our election campaign," he told a press conference, adding that "defects" had been found in the approval given by his predecessor in 2013.
The central government will for now continue its work in the district, but it will "handle the situation based on the law," said Chief Cabinet Secretary Yoshihide Suga in a morning press conference.
The move comes after Tokyo resumed work in Henoko Saturday following a month-long suspension as talks continued with local officials opposed to the project, and residents staged a protest.
Both Tokyo and Washington have repeatedly backed the plan, with Prime Minister Shinzo Abe last month insisting it was "the only solution".
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