Governor Takeshi Onaga has accused Abe of looking down on Okinawa, amid a deepening row that has sparked demonstrations of support by tens of thousands of protesters around Japan in recent months.
The government`s decision to sue Onaga follows his refusal to reinstate approval, which he had withdrawn last month, for key landfill work needed for the base move. The original permit had been granted by Onaga`s predecessor.
Should the court decide in favor of the central government, it would give land minister Keiichi Ishii the power to override Onaga`s opposition.
"We`re a nation of laws, and so we proceed according to the judgment of law," Chief Cabinet Secretary Yoshihide Suga told a news conference. "This was the unavoidable result."
Onaga told reporters only that he "would respond firmly."
Perceptions of bullying from Tokyo could dent support for Abe, already struggling with an economy back in recession, before key elections next year.
The United States and Japan agreed in 1996 to close Futenma. The central government says the base is one of the "most dangerous airports in the world" because of its location in a densely populated area, but plans to move it stalled due to opposition from Okinawa residents worried about noise, pollution and crime.
Political analyst Atsuo Ito said it was now difficult to see where the two sides could compromise, and that it may be hard to force construction through due to public opinion.
"The government`s biggest fear is that protests will grow violent and somebody will be hurt or even killed," he said.
"If the general Japanese public really takes Okinawa`s side, this will be bad for the government, and an incident would make things blow up."
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