The troops were aboard three vessels that arrived at the central Philippine port of Cebu, an official at the Japanese embassy said, in what is the biggest overseas deployment of Japan's military since its defeat in World War II.
They will join a huge international relief effort to help survivors of Super Typhoon Haiyan, which flattened dozens of towns through the central Philippines on November 8, leaving at least 5,500 dead or missing.
Japan's contribution to the humanitarian effort comes as a newly-confident Tokyo looks to make its mark again on the world order, after decades in which the idea of its troops on foreign soil was complete anathema.
In many parts of Asia, memories linger of the brutality of invading Japanese soldiers prosecuting an expansionist romp through the region in the name of the emperor.
In a twist of historic irony, the Japanese troops are returning to areas of the Philippines that saw Japan lose one of history's biggest naval battles to the US-led Allies.
"We were hiding in holes dug under the floor of our homes," she recalled. "The Japanese soldiers were patrolling but we couldn't see much of them. We could only see their boots. We were so afraid."
But Macaya, who was waiting for treatment at a temporary field clinic set up by the Japanese government in Tacloban, the typhoon-ruined capital of Leyte, said she was very pleased the former occupier was back.
"I don't hold any grudges anymore. There's no more bad blood between us," she said.
He declared himself "happy" there were Japanese boots back on Philippines soil.
"There's nothing like two allies living in harmony with each other," he said.
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