The lawsuit by Okinawa prefecture comes after the central government sued it last month 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 percent of US military facilities in the country.
Earlier this week, Okinawa governor Takeshi Onaga renewed his pledge to prevent the central government from building a US Marine base in a remote part of the island to replace the existing Futenma facility in a heavily populated area.
"Taking every possible measure, I will not let (the central government) construct the base," Onaga said.
In October, Onaga cancelled a 2013 approval for the project by his predecessor, saying it was not legally sound, prompting Tokyo to seek court action.
Okinawa's suit, filed in the prefectural capital of Naha, asks the court to revive his cancellation order of a landfill permit, which is currently nullified by the central government, court and local officials said.
Chief Cabinet Secretary Yoshihide Suga described the latest legal action as "extremely regrettable," insisting the initial approval was legal and formed a precedent that allows landfill work to continue.
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 United States first proposed moving Futenma in 1996, though both insisted it must remain in Okinawa -- a key area from which US troops and aircraft can react to potential conflicts throughout Asia.
But residents have insisted Futenma should be closed and a replacement built elsewhere in another part of Japan or overseas, saying they can no longer live with the noise pollution, accidents and occasional crimes committed by US service members.