The dispute over the relocation of U.S. Marine Corps Air Station Futenma to another site in Okinawa has finally developed into a court battle between the national government and the prefecture that hosts the bulk of the U.S. military presence in Japan. The Abe administration appears confident that it can override the local opposition to building the replacement facility off the Henoko area of Nago. But it should also think about the long-term impact a full-blown legal confrontation with the prefectural government would have on Okinawa’s sentiment toward the U.S. bases and possibly the bilateral security alliance itself.

The government on Tuesday filed a lawsuit with the Naha branch of the Fukuoka High Court, seeking a court judgment to empower itself to override Okinawa Gov. Takeshi Onaga’s recent revocation of permission given in 2013 by his predecessor to work on reclaiming land off Henoko to build the new airfield to replace the Futenma base in Ginowan, central Okinawa. If the court decides in its favor and the ruling is finalized, the government plans to act on behalf of the governor to withdraw his revocation and go ahead with the project.

It is the latest development in the relocation of Futenma, which was originally agreed on between Japan and the United States way back in 1996 — on condition that a new replacement facility would be built in Okinawa, but it’s the first time the matter has been taken to court. Okinawa Prefecture has separately filed a complaint with a third-party organ that settles disputes between national and local governments against a decision by the land minister to suspend the validity of Onaga’s revocation of the reclamation permit, and is also ready to take the matter to court if its argument is not upheld.

The Futenma relocation made little headway even after the national government decided on the Henoko area as the site of the new facility in 1999. Local opposition to the plan hardened after Prime Minister Yukio Hatoyama, who headed a Democratic Party of Japan-led government that ousted the Liberal Democratic Party from power in 2009, said his administration would seek to build the replacement facility outside of Okinawa — only to revert to the original plan months later.

After the LDP returned to power under Prime Minister Shinzo Abe, the government succeeded in getting then-Gov. Hirokazu Nakaima — who earlier pledged in his re-election campaign to move the Futenma replacement facility outside of the prefecture — to give the go-ahead in 2013 for reclamation of land off Henoko, upon promises of hefty government spending to spur Okinawa’s economy. But Nakaima’s about-face cost him the support of voters, and he was defeated in the November 2014 gubernatorial race by Onaga, who had promised to do everything in his capacity to stop the Henoko construction.

The Abe administration, meanwhile, went ahead with the project, launching seabed-drilling work off Henoko a few months before Nakaima was ousted in the November election. While it temporarily halted the work this summer for a series of brief talks with the prefectural government, the administration essentially maintained that Nakaima’s approval stands legitimate irrespective of Onaga’s challenge to it, and that building the new facility off Henoko is the only solution to removing the danger posed by the Futenma base, located in the middle of a residential area. Even as it offered a dialogue with Okinawa, the government did not appear willing to budge from its position.

When Onaga finally revoked the reclamation permit last month, citing “legal flaws” in his predecessor’s decision, the administration responded by suspending the validity of the revocation — in a procedure questioned by some experts for its fairness because a government body, the land ministry in this case, was acting on a complaint filed by another part of the government: the Defense Ministry’s local bureau, thus enabling the government to continue the reclamation work.

In filing the lawsuit Tuesday, the national government claimed Onaga’s decision to revoke the reclamation permit was illegal because the disadvantages that would be caused by the move to put the Futenma relocation on hold — including potential damage to the trust between Japanese and U.S. governments, and to Japan’s diplomatic, defense and other national interests — trump the losses that Okinawa claims it will suffer if the permit stands. The government also charged that Onaga’s challenge to the rationale of building a Futenma replacement facility on another site in Okinawa is irrelevant because a prefectural governor has no power to judge on matters of national security concern, such as where to station a U.S. military base.

The government may be confident of winning the court battle with Okinawa — as it did 20 years ago when Gov. Masahide Ota, amid a flare-up of strong anti-U.S. base sentiment triggered by the rape of a schoolgirl by U.S. servicemen, declined to sign documents for the seizure of land to be used by U.S. bases from landowners who refused to put up their property for lease. A suit filed by the government seeking to override Ota’s refusal quickly ended in a court order for the governor to sign the document, citing damage to the public interest.

But by taking the matter to court, the government has abandoned its efforts to close the sharp divide between its policy and the popular will in Okinawa, which in recent elections has clearly demonstrated its opposition to the Henoko project. The court battle could complicate the standoff even further, and a ruling in favor of the national government likely won’t change local sentiment — in which case there is no guarantee that a final solution to the protracted issue of Futenma’s relocation can be reached.

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