Hauling guano by muscle-power in the fierce tropical heat, combined with general disgruntlement with conditions on the island, eventually provoked a rebellion in 1889, in which five supervisors died. A U.S. warship returned eighteen of the workers to Baltimore for three separate trials on murder charges. A black fraternal society, the Order of Galilean Fisherman, raised money to defend the miners in federal court, and the defense built its case on the contention that the men acted in self-defense or in the heat of passion, and that the United States did not have jurisdiction over the island.
The cases, including Jones v. United States, 137 U.S. 202 (1890) went to the U.S. Supreme Court in October 1890, which ruled the Guano Act constitutional, and three of the miners were scheduled for execution in the spring of 1891. A grass-roots petition driven by black churches around the country, also signed by white jurors from the three trials, reached President Benjamin Harrison, who commuted the sentences to imprisonment and mentioned the case in a State of the Union Address. Guano mining resumed on Navassa at a much reduced level. The Spanish–American War of 1898 forced the Phosphate Company to evacuate the island and file for bankruptcy, and the new owners abandoned the island after 1901.
Navassa became significant again with the opening of the Panama Canal in 1914. Shipping between the American eastern seaboard and the Canal goes through the Windward Passage between Cuba and Haiti. Navassa, a hazard to navigation, needed a lighthouse. The U.S. Lighthouse Service built Navassa Island Light, a 162-foot tower on the island in 1917, 395 feet above sea level. A keeper and two assistants were assigned to live there until the Lighthouse Service installed an automatic beacon in 1929.
After absorbing the Lighthouse Service in 1939, the U.S. Coast Guard serviced the light twice each year. The U.S. Navy set up an observation post for the duration of World War II. The island has been uninhabited since then. Fishermen, mainly from Haiti, fish the waters around Navassa.
A scientific expedition from Harvard University studied the land and marine life of the island in 1930. After World War II amateur radio operators occasionally visited to operate from the territory, which is accorded “entity” (country) status by the American Radio Relay League. The callsign prefix is KP1. From 1903 to 1917, Navassa was a dependency of the U.S. Guantanamo Bay Naval Base, and from 1917 to 1996 it was under United States Coast Guard administration.
In 1996 the Coast Guard dismantled the light on Navassa, which ended its interest in the island. Consequently, the Department of the Interior assumed responsibility for the civil administration of the area, and placed the island under its Office of Insular Affairs. For statistical purposes, Navassa was grouped with the now-obsolete term United States Miscellaneous Caribbean Islands and is now grouped with other islands claimed by the U.S. under the Guano Islands Act as the United States Minor Outlying Islands.