Major Reynaldo Balido, spokesman for the national disaster risk reduction and management council, said six people died in the Compostela Valley province.
Seven other people died in Davao Oriental province, including five who perished in a landslide in the township of Tarragona.
The flooding has affected 132,000 people from 10 provinces, but it is still unclear how many of them have had to evacuate their homes, he added.
Liza Mazo, a regional disaster response official, said 10,000 people fled to safer ground in her region that covers four provinces and an island after two days of rains flooded low-lying villages and set off minor landslides.
The same area was hit by a typhoon in December 2012, leaving 2000 people dead.