Susumu Inamine, 68, won re-election Sunday, dealing a blow to the central government's plans to build a replacement Marine air base in the environmentally sensitive Henoko district, Japan Times reported.
"This election was easy to understand. It was about one issue, the Henoko issue, and whether you were for or against the new base," Inamine said after the final ballot count.
"The people have spoken and they have said no."
His re-election will be a headache for Prime Minister Shinzo Abe's government and comes after Okinawa Gov. Hirokazu Nakaima granted Tokyo permission in late December to proceed with a base-related landfill project in Henoko Bay, near Nago.
Inamine's supporters claim Abe and Nakaima reached a backroom deal to allow relocation of the base in exchange for $3.32 billion in development assistance this year and nearly $3 billion annually for Okinawa until 2021, the Japan Times reported.
Abe's Cabinet ministers expressed confidence that the relocation will proceed as planned, Kyodo news agency reported.
Chief Cabinet Secretary Yoshihide Suga said Inamine's re-election was "very disappointing," but he can do little to block construction.
"The central and local governments are on the same page, that the plan is the only solution to removing the danger of keeping the Futenma base [in a densely populated area] while maintaining deterrence," Suga said.
Japanese Defense Minister Itsunori Onodera said relocation would continue, the BBC reported.
"We hope to make steady progress on the relocation plan in order to eliminate risks posed by Futenma," he said.
"It was a local election and I don't think it will immediately have a direct impact on the relocation issue."
Relocation of the Futenma base in Ginowan city is an emotional issue, where anti-base sentiment is high amid safety concerns about U.S. military operations.
Calls for the base relocation also strengthened after three U.S. servicemen raped an Okinawa school girl in 1995.
Even though people in Ginowan want the base relocated, they also know thousands of jobs would be lost.
The U.S. bases are a legacy of World War II when U.S. forces captured the island chain on their way to defeating Japan.
In 1972 the U.S. government returned the islands to Japanese administration, but air safety issues have increased calls for relocating the the base.
Since the return of Okinawa to Japanese authority in 1972, 44 crashes involving U.S. military aircraft have occurred, leaving 84 people dead, injured or missing, Asahi Shimbun reported.
Asahi Shimbun reported in August an HH-60 helicopter from the U.S. Marine base in Kadena on Okinawa crashed in a training area on the Marines' Camp Hansen base. There were no casualties.
In August 2004, a U.S. helicopter crashed into the grounds of Okinawa International University. There were no casualties except for minor injuries to the three U.S. crewmen.
Maintaining a presence in Okinawa in Japan's Ryukyu Island chain and about 400 miles south of the Japanese mainland is strategically important for the United States and its alliance with Japan.
Okinawa is relatively close to China at a time when Beijing is expanding its naval power including the deployment of the country's first aircraft carrier.
But Okinawa is less than 500 square miles and has a population of about 1.5 million people. More than a dozen U.S. bases on the island have a third of the 38,000 U.S. military personnel stationed in Japan.
Critics of the U.S. bases on Okinawa say the island has a disproportionate number of U.S. personnel given the island's small size.
The United States and Japan agreed in 2012 to start reducing the number of U.S. military personnel on the island, The Washington Post reported at the time.
About 9,000 U.S. personnel eventually will leave for other bases in Japan, leaving about 10,000 Marines on Okinawa.