Chief government spokesman Yoshihide Suga expressed his condolences, praising Mr Onoda for his strong will to live.
The intelligence officer came out of hiding on Lubang island in the Philippines in March 1974 and surrendered only when his former commander flew there to reverse his 1945 orders to stay behind.
Mr Onoda and another wartime holdout, Sgt Shoichi Yokoi, who emerged from the jungle in 1972, received massive heroes' welcomes upon returning home.
In his formal surrender to then Philippines president Ferdinand Marcos, Mr Onoda wore his 30-year-old imperial army uniform, cap and sword, all still in good condition.
"I don't consider those 30 years a waste of time," Onoda said in an interview in 1995. "Without that experience, I wouldn't have my life today."
Onoda worked for a Japanese trading firm in Shanghai after finishing school in 1939. Three years later, he was conscripted and trained at a military academy.
In December 1944, he was sent to Lubang, about 90 miles southwest of Manila. Most other Japanese soldiers surrendered when US troops landed on Lubang in February 1945, though hundreds remained missing for years after the war.
As he struggled to feed himself, Onoda's mission became one of survival. He stole rice and bananas from local people down the hill, and shot their cows to make dried beef, triggering occasional shooting at each other.
The turning point came on February 20 1974, when he met a young globe-trotter, Norio Suzuki, who ventured to Lubang in pursuit of Onoda.
Suzuki returned to Japan and contacted the government, which located Onoda's superior, Major Yoshimi Taniguchi, and flew him to Lubang to deliver his surrender order in person.