The lawsuit was filed against Okinawa Governor Takeshi Onaga, seeking the court's confirmation that Onaga acted illegally in not complying with a state order to retract his revocation of former governor's permission for the landfill work of the Futenma air base relocation, Xinhua news agency reported.
The lawsuit will reopen a legal battle between the governments, which was first ignited last year when they sued each other over the issue, and was halted in March when a settlement deal was reached under the court mediation.
The construction work was halted as they awaited a ruling by an arbitration panel under the internal affairs ministry.
However, the panel failed to reach a conclusion in June and urged the two sides to hold more "sincere discussions".
During a negotiation meeting on Thursday, Okinawa indicated that it would not file a fresh lawsuit, while the central government said it would take the issue to court again, in an apparent effort to push forward the relocation work.
The government is fulfilling its obligations under the terms of the March settlement by proceeding with the lawsuit, a spokesman confirmed.
But for Onaga, what the central government has done is "intolerable" and "is far from how a democracy should be", for it "fiercely proceeded" with the construction of the replacement facility despite opposition from local people.
Meanwhile, the Japanese government resumed the construction work of a number of helipads for the US military in Okinawa on Friday, a move further adding fuel to the people's resentment and anger.
On Friday, some 100 local residents and other protesters gathered in front of the construction site, protesting against the relocation plan and seeking to block the entry of construction workers by lying on the road and parking their cars there, citing possible safety and noise problems caused by the helipads.
In 1996, US agreed to return Japan the half of its military training area in northern Okinawa. According to the agreement, the six helipads to be returned shall be relocated to the area retained, out of which two already have been constructed.
On July 11, just one day after Japan's upper house election, the Defence Ministry's Okinawa Defence Bureau abruptly started moving construction materials and equipment into the area, stirring up tension in the region.
Anti-US base sentiment has been high in Okinawa, especially after a former US marine working as a civilian employee at the Kadena Air Base was arrested in May for raping and murdering a local woman.
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