They attended a rally in Japan's southern island of Okinawa to protest the American presence there, BBC News reports.
Under a 2006 agreement, the Marine Corps Air Station Futenma was to be relocated from the center to the coast but demonstrators want Prime Minister Yukio Hatoyama to honor his election pledge to move it off the island.
The row has strained relations between Japan and the United States.
"Mr. Hatoyama has failed completely as a Japanese politician, as a leader of this country to take control of that issue," Keith Henry, principal officer at Asia Strategy in Tokyo, told CNN. "What should have been a regional issue within Okinawa has become a national referendum on Hatoyama himself, and unfortunately, on the state of U.S.-Japan relations."