Hundreds of people participated in the demonstration, sitting or lying on the ground in the road to Camp Schwab in an effort to prevent vehicles transporting building materials from accessing the site.
"Don't lend a hand in the construction of the military base!" the crowd chanted as they were dragged away.
For two decades the military has been wanting to move the Marine Corps Air Station Futenma Okinawa base further north in Okinawa.
The plan to relocate the installation has drawn protests by tens of thousands of residents who worry about sexual assaults by US service members, violence, and the environmental impact on local ecosystems.
Over 50,000 US military personnel currently reside in Japan, and more than half of those live in Okinawa.
"Don't the people of Okinawa have sovereignty?" 70-year-old Katsuhiro Yoshida, an Okinawa prefectural assembly member, told the Asahi Shimbun. "This reminds me of the scenes of rioting against the U.S. military before Okinawa was returned to Japan (in 1972). Now we are facing off against our own government. It is so contemptible."
The current governor of Okinawa, Takeshi Onaga, was elected on the premise that he would not allow the base to be constructed. He made good on that pledge, until Japan’s land ministry announced this week that they were overring his decision.
"The fact that they forcibly executed this construction, there is nothing but anger," Takashi Kishimoto from the Okinawa Peace Movement Center told NBC News. "We are outraged at these political tactics which ignore will of the people."
A poll conducted by the Okinawa Times found that 76% of residents are opposed to the construction of a new base.