TOKYO — A long-running political dispute in Japan over the proposed relocation of a United States Marine Corps air base entered new territory on Tuesday, after the governor of Okinawa revoked permission for construction work to take place at the site planned for the facility.

The decision, which central government officials in Tokyo said they would appeal, is the latest setback for a 20-year effort by Japanese and American military planners to move the base, Marine Corps Air Station Futenma, from its current location in the middle of a crowded Okinawan city to a less populated part of the island.

Conflict over the base has grown more acute under Prime Minister Shinzo Abe, who has pledged to complete the site for the Marines on Henoko Bay — a goal that has eluded numerous predecessors. Tokyo and Washington agreed on the relocation in the 1990s, but popular opposition in Okinawa has prevented the deal from being carried out. Many residents want the American military presence on their small southern island reduced, not simply redistributed.

Mr. Abe has risked political resistance by reviving the relocation project, which is part of his broader focus on national security. Mr. Abe’s agenda, partly driven by concerns over the growing military power of China, is hawkish for a Japanese leader: Along with bolstering Japan’s already strong defense ties to the United States, he has lifted restrictions on arms exports, reversed a long decline in military spending and — most contentious — reinterpreted the pacifist Constitution to allow Japanese forces to undertake some types of combat missions overseas.