Okinawa governor Takeshi Onaga had tried to block efforts to reclaim land for the new offshore facility.
The Japanese and US governments want the Futenma airbase located in a crowded city on the island moved to a sparsely populated area in the north for safety reasons. But many Okinawans want it off the island altogether.
Okinawa governor Takeshi Onaga had tried to block efforts to reclaim land for the new offshore facility and he and Prime Minister Shinzo Abe filed rival lawsuits to try to settle the issue.
But in December the Supreme Court ruled in favour of the central government, giving the green light to move ahead on construction.
"The government's position was entirely supported by the Supreme Court ruling," top government spokesman Yoshihide Suga told a regular briefing on Monday.
He said that during a visit Friday and Saturday by US Defense Secretary James Mattis, the two sides reaffirmed that the new facility "is the only solution".
Japanese TV footage showed construction vessels carrying gigantic concrete blocks offshore, where workers will soon start dropping them into the water for landfill purposes.
Tokyo and Washington first proposed moving the Futenma airbase, a Marine Corps facility located in the middle of the city of Ginowan, in 1996. But the plan has been mired in local opposition.
Campaigners want a replacement built elsewhere in Japan or overseas, saying they can no longer tolerate the heavy American military presence on Okinawa due to noise, accidents and crimes by US service members.
On Monday dozens of protesters were seen trying to block heavy trucks and machines from entering the construction site, scuffling with riot police.
Okinawa, which accounts for less than one percent of Japan's total land area, hosts about 28,000 US troops -- more than half of the approximately 47,000 American military personnel stationed in Japan.
Islanders have complained for decades that the rest of the country ignores their burden.
"Does the government really see Okinawans as Japanese? I am extremely angry," said Susumu Inamine, mayor of the city of Nago that has jurisdiction over the construction area.