The dispatch of the Self-Defense Forces emergency relief team comes as the government of Prime Minister Shinzo Abe is pushing to ease limits on the military imposed by its post-war, pacifist constitution.
Japan invaded the Philippines in World War Two and scattered fighting continued until Tokyo's surrender in 1945, but Philippine officials have said their nation does not share the concerns of others in Asia, notably China and South Korea, about Japan's military past.
The Philippines, like Japan a strong ally of the United States, has also said it views Japan as a counterweight to the increasing regional role of China.
Chief cabinet secretary Yoshihide Suga said the decision to send the troops followed a request from Manila. He also said Tokyo would provide $10 million in emergency aid.
"We hope to make every effort to get the aid to the people who need it as soon as possible," he told a news conference, adding that the number of troops will be increased if the situation on the ground warrants it.
Timing of the dispatch was being coordinated with the Philippines, but the troops were ready, Suga added. A team of 25 people, mainly medical workers, left for the Philippines on Monday.
Disaster relief activities both at home and abroad by the Self-Defense Forces have gone a long way to improve the military's domestic image. About 1,000 soldiers and other personnel took part in relief efforts in Aceh after the 2004 tsunami, and troops went to Haiti following a devastating earthquake in 2010.
Expanding such non-combat activities is a key part of Abe's campaign for a more proactive role for the military overseas.
He is pushing for lifting a self-imposed ban on exercising the right of collective self-defense, or aiding an ally under attack, a much more controversial move. He has pledged to bolster the military to cope with what Japan sees as an increasingly threatening security environment, including an assertive China and an unpredictable North Korea.
"Japan's dispatch of its self-defense forces is strictly confined," said Shinichi Kitaoka, who heads an advisory panel expected to recommend at least a partial lifting of the ban on collective self-defense.
"We have started to go to many places nowadays, Haiti and other places. So to me, Japan's expansion to the more active participation in peace maintenance is a natural trend."
(Reporting by Elaine Lies and Linda Sieg; Editing by Nick Macfie)
