Horie, who was prisoner of war in Rabaul in 1945, has travelled to Papua New Guinea 18 times and is a former Member of Parliament in Japan.
O'Neill was in Japan for the 8th Pacific Islands Leaders Meeting, which was held in Iwaki City, Fukushima Prefecture, on May 18 and 19.
"It was an honour to meet Mr Horie tonight. His tireless efforts to bring his countrymen home is outstanding and has earned him the highest respect in both of our countries.
"Papua New Guinea is the final resting place of so many courageous men and women from both sides of the war," O'Neill said.
"Our nation will always accord the highest respect to those still buried in our soil.
"We will continue to work closely with Japan in their efforts to repatriate the remains of the fallen, and return them to their homeland."