However, they have so far been unable to arrange a meeting with the pair.
Prime Minister Junichiro Koizumi’s spokesman, Yu Kameoka, told reporters they were apparently reluctant to meet with the diplomats at a hotel in the port city of General Santos because of the large crowds waiting to see them.
Authorities were trying to schedule another meeting for today.
Media reports in Japan said the men, now in their 80s, lived on the southern island of Mindanao with equipment suggesting they were former soldiers.
One report said they were separated from their division and later wanted to return to Japan but feared they would face a court-martial.
Mr Koizumi said in Tokyo he hoped the mystery would be cleared up soon.
“We are checking it now,” he said. “It is a surprise if it’s true, but we have to check first.”
Goichi Ichikawa, the chairman of a veterans group in Japan, said he had learned of at least three Japanese men living in the mountains of Mindanao from someone who went there late last year and alerted Tokyo in February.
“It’s amazing they were able to survive for 60 years,” Mr Ichikawa said. “Of course I was stunned.”
The reports were reminiscent of Second World War straggler Lieutenant Hiroo Onoda, who believed the war was still on when he was found in the jungles of the Philippines in 1974.
He refused to give up until March of that year, when the Japanese government flew in his former commander to formally tell him that the war was over.
Japan’s Kyodo News agency said the two may be Yoshio Yamakawa, 87, and Tsuzuki Nakauchi, 83. But the health ministry in Tokyo declined to confirm this.
The Japanese newspaper Sankei Shimbun said the two had been in the mountains of Mindanao for about 60 years.
They remained there after losing their division in the mountains, the paper said. Last September, a Japanese national in the lumber business ran into them in the mountains. It was learned later that they wanted to go back to Japan but were afraid of facing a court-martial for withdrawing from action.
Another source said that there may be more than 40 other Japanese soldiers living in the mountains and that they all want to return to Japan.
Japan’s Health Ministry, in charge of repatriating Japanese overseas, said it was sending an official to General Santos, about 600 miles south of Manila, to try to schedule another meeting with the pair.