SEOUL, South Korea — Japanese prosecutors have indicted a U.S. serviceman in Okinawa for kidnapping and sexually assaulting a Japanese minor, a crime that looks set to reignite Okinawan grievances against both the American presence on the strategic island and the central government in Tokyo.

The crime was allegedly committed by U.S. Airman Brennon Washington, 25, on Dec. 24. He invited the victim, an unnamed girl who was under 16 at the time, to speak to him, then drove her to his residence where, prosecutors say, he assaulted her.

Though the crime took place in December, Airman Washington was not indicted until March 27. Fueling the controversy, Okinawa Prefecture was only notified of the indictment on June 26, when Japan’s media reported the incident.

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Three days before the news broke, on June 23, Japanese Prime Minister Fumio Kishida had visited Okinawa to commemorate the 79th anniversary of the fierce battle fought on the island in the closing months of World War II. Today, the prefecture accounts for less than 1% of Japan’s land area, but hosts 70% of facilities exclusively used by the U.S. military.

During his visit, Mr. Kishida, a staunch American ally, admitted that Okinawans “bear a heavy burden” in hosting the largest contingent of U.S. troops in Japan.

Okinawa’s governor, who long opposed the U.S. base presence, has questioned both the reported crime and the delay from Japan’s Foreign Ministry in communicating it to local officials. Sexual crimes by G.I.s against Japanese minors in Okinawa in 1995 and 2008 generated major public outrage.

“Not only does it cause anxiety among the residents of the prefecture, who are forced to live side by side with the base, but it also tramples on the dignity of women, especially considering the fact that the victim is a minor,” Okinawan Governor Denny Tamaki said Tuesday.

Noting the delay in revealing the legal case, Mr. Tamaki added, “The lack of communication can only cause distrust.”

The first court hearing in Airman Washington’s case is set for July 12.

The controversy may deliver a needed political boost to the governor. Parties that backed his position against U.S. troops lost their majority in the Okinawan Prefectural Assembly elections on June 16.

Mr. Tamaki’s hostility to the U.S. military presence has created friction with national authorities in Tokyo, who increasingly see Okinawa and the smaller islands in the Ryukyu Chain as strategically vital. The Japanese Asahi Daily newspaper headlined its story on the prime minister’s recent visit: “Kishida, Tamaki still worlds apart on Okinawa memorial day.”

While Tokyo is working to relocate U.S. Marine Air Station Futenma from a densely populated part of the island to the coast, Mr. Tamaki and his supporters want the base to leave Okinawa altogether.

Speaking at the memorial to the 1945 battle last weekend, Mr. Tamaki said, “The ongoing rapid expansion of the [Japanese] Self-Defense Forces’ deployment, coupled with the memories of the tragic Battle of Okinawa, have made the people of Okinawa deeply anxious.”