The Naha district court's Okinawa branch handed down the ruling, public broadcaster NHK reported.
Some 22,000 residents from five municipalities around the US Kadena Air Base, the largest US base in Far East Asia, filed suit against the state in 2011.
They demanded compensation for damages and the suspension of flights during the night and early morning. They said aircraft noise disrupted their sleep and caused health damages.
The government argued that there was no concrete proof of noise causing health problems.
Presiding Judge Tetsuya Fujikura acknowledged almost all the plaintiffs' claims of damages caused by aircraft noise.
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The judge said noise from the base has been an issue since around 1970.
However, the government has failed to take major steps to deal with the problem, allowing unlawful noise pollution to continue.
But the judge turned down the residents' request to ban flights. He said that under the Japan-US Security Treaty and other agreements, the government was not in a position to regulate US military aircraft operations.
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Lawyers for the residents say it is the largest amount the government has been ordered to pay in a lawsuit over noise from bases, the public broadcaster added.
It exceeds the previous record, for a lawsuit over noise from the Atsugi airbase shared by US forces and Japan's Self-Defence Forces near Tokyo.
Plaintiffs in that trial were awarded nearly $80 million in damages in December 2016.