Nearly 1,000 people were killed after Typhoon Washi hit southern Mindanao island and surrounding areas at the weekend.
Mr Aquino has declared a national calamity and said the priority must now be the tens of thousands left homeless.
Some cities plan to conduct mass burials of unidentified bodies on Tuesday amid growing health concerns.
Disaster agencies are attempting to provide food, water, medicine and body bags, but damaged roads are hampering efforts to reach survivors in remote villages.
Mr Aquino was flown over the coastal region to see the scale of the destruction, before meeting survivors and local officials.
After widespread criticism that the authorities were caught unprepared, he promised a full review into disaster plans, to ensure such devastation could not happen again.
“First priority is to relocate to areas that no longer pose a danger to them,” he told a meeting in Cagayan de Oro, where nearly 600 people lost their lives as flash floods hit early on Saturday.
A spokesman for the president, Ricky Carandang, said declaring a national calamity would enable the government to direct more funds to the relief effort, Reuters reports.
The BBC’s Kate McGeown in the region said the authorities now face a massive task as unclaimed bodies pile up at mortuaries. Some authorities are reported to have run out of coffins.