Two people were reported missing in high water that inundated villages, the Philippine Daily Inquirer reported.
About 27,000 people were affected by the rising water and more than 5,000 families were in evacuation centers, civil defense officials said.
Rain falling non-stop since Saturday overflowed the banks of the Tamugan River, one of the main tributaries of the Davao River.
At least 12 villages along the Davao River were flooded.
Classes were called off in all schools in Davao City.
The flooding is considered among the worst the city has had in recent years.