A total of 1,002 people have been confirmed dead, including 650 in Cagayan de Oro and 283 in nearby Iligan city.
A tropical storm swept through the area last Friday night, unleashing flash floods that caught most of the victims in their sleep.
President Benigno Aquino declared a state of national calamity during a visit to the region on Tuesday and promised the government “will do its best to prevent a repeat of this tragedy”.
He said there would be an assessment of why so many people died and why those living along riverbanks and close to the coast, most of them illegal settlers, had not been moved to safety.
Illegal logging is another factor believed to have contributed to the staggering death toll, as many victims were swept away by huge logs that rolled down denuded mountains facing the two cities.
Mr Aquino declared a ban on logging in February, but weak law enforcement and corruption make it a recurring problem.