After moving to Jakarta, Latuharhary also began working for the Japanese under the Department of Home Affairs to manage the Moluccans in Java, and held responsibility for their actions. In 1944, a group of Ambonese including Latuharhary were arrested by the Kenpeitai and brought to Bogor as they were suspected of espionage for the Allied forces, and due to the fact that Latuharhary had partly used his position within the Japanese administration for political purposes. However, his wife and two others again managed to convince a Japanese Navy commander to arrange for their release. In late 1944, he was again arrested after a Moluccan prisoner escaped from a prison. Japanese authorities at the time were particularly suspicious of Ambonese after the Battle of Morotai and the strategic bombing of Ambon in 1944, further fueled by Allied espionage operations in the Moluccas led by Ambonese Julius Tahija.