Onoda died in a Tokyo hospital Thursday, Kyodo News reported.
Onoda returned to Japan in March 1974 after remaining on Lubang Island in the northwestern Philippines for nearly 29 years after the end of the war because he was unaware that Japan surrendered. In 1975, he emigrated to Brazil, where he ran a farm.
Since 1984, he organized "Onoda Shizen Juku" -- or Onoda Nature School -- throughout Japan for nature and life education.
Chief Cabinet Secretary Yoshihide Suga said during a news conference, "I vividly remember that I was reassured of the end of the war when Mr. Onoda returned to Japan."
As related in his memoir, Onoda, a 2nd lieutenant, received his last order in early 1945 -- to stay and fight on Lubang Island, the New York Times reported.
Onoda, an intelligence officer trained in guerrilla warfare, and three enlisted men found leaflets about the war's end but thought they were propaganda, his memoir said. They built huts, ate bananas, coconuts and rice stolen from a village, and killed animals for meat. They patched their uniforms and kept their weapons in working order.
They evaded American and Filipino search parties and attacked islanders they considered enemies, killing about 30 people in the intervening years, the Times said. One of the enlisted men surrendered to Filipino forces in 1950, and two others were shot and killed by island police officers searching for them, one in 1954 and another in 1972.
Onoda, officially declared dead in 1959, was found by Norio Suzuki, a student searching for him in 1974, the Times said. Insisting he was waiting for orders, Onoda rejected Suzuki's plea to leave until Suzuki returned with photographs and the Japanese government sent a delegation to formally relieve him of duty.
In Manila, the lieutenant, wearing his mended uniform, presented his sword to President Ferdinand Marcos, who pardoned him for crimes committed while he thought he was at war.