The lawsuit comes amid a long-running drama between Tokyo, keen to satisfy security ally the United States, and Okinawa, where frustration over a seven-decade American military presence is rife.
Pacifist sentiments run high on the island that accounts for less than one percent of Japan's total land area but hosts about 75 per cent of US military facilities in the country.
Takeshi Onaga, Okinawa's governor, has said he would "do his best" to prevent the central government from building a new US Marine base in a remote part of the island to replace the existing Futenma facility in a heavily populated area.
The central government's suit, filed in the Okinawan capital of Naha, is asking the court to void Onaga's cancellation order of a landfill permit needed to construct the facility.
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"The legal action was necessary in order to remove danger associated with the Futenma air base," Chief Cabinet Secretary Yoshihide Suga, told reporters.
Suga was referring to the existing marine base located in the central Okinawan city of Ginowan and widely seen as a danger to residents.
The Okinawan prefectural government had no immediate comment but said Onaga was likely to issue a statement later.
Work in the Henoko district of Nago city in the island's north is only in the initial stages, with crews setting up sea floats and a makeshift bridge necessary for the landfill work.
Japan and the US first proposed moving Futenma in 1996, though insisted it must remain in Okinawa -- a key area from which US troops and aircraft can react to potential conflicts throughout Asia.
American and Japanese troops fought a bloody battle on Okinawa in 1945, with the US subsequently occupying the island for 27 years before handing it back to Japan.