Hiroo Onoda waged a guerrilla campaign in Lubang Island near Luzon until he was finally persuaded in 1974 that peace had broken out, ignoring leaflet drops and successive attempts to convince him the Imperial Army had been defeated.
He died in a Tokyo hospital on Thursday of heart failure.
Onoda was the last of several dozen so-called hold-outs scattered around Asia, men who symbolised the astonishingly dogged perseverance of those called upon to fight for their emperor.
Their number included a soldier arrested in the jungles of Guam in 1972.
Trained as an information officer and guerrilla tactics coach, Onoda was dispatched to Lubang in 1944 and ordered never to surrender, never to resort to suicidal attacks, and to hold firm until reinforcements arrived.
He and three other soldiers continued to obey that order long after Japan’s 1945 defeat.
Their existence became widely known in 1950, when one of their number emerged and returned to Japan.
The others continued to survey military facilities in the area, attacking local residents and occasionally fighting with Philippine forces, although one of them died soon afterwards.
Tokyo declared them dead after nine years of fruitless search.
However, in 1972, Onoda and the other surviving soldier got involved in a shoot-out with Philippine troops. His comrade died, but Onoda managed to escape.
The incident caused a sensation in Japan, which took his family members to Lubang in the hope of persuading him that hostilities were over.
Onoda later explained he had believed attempts to coax him out were the work of a puppet regime installed in Tokyo by the US.
He read about his home country in newspapers that searchers deliberately scattered in the jungle for him to find, but dismissed their content as propaganda.
The regular overflight by US planes during the long years of the Vietnam war also convinced him the battle he had joined was still being played out across Asia.
It was not until 1974, when his old commanding officer visited him in his jungle hideout to rescind the original order that Onoda’s war ended.
Asked at a press conference in Japan after his return what he had been thinking about for the last 30 years, he told reporters: “Carrying out my orders.”
But the Japan that Onoda returned to was much changed. The country he had left, and the one he had believed he was still fighting for, was in the grip of a militarist government, bent on realising what it thought was its divine right to dominate the region.
Its economy was in ruins and its people were hungry.