Elmeir Apolinario, a spokesperson for the office, said four died from the landslides and one from drowning.
He said the heavy downpour on July 12 night triggered two landslides and massive flooding in the city, affecting at least 4,000 families.
Zamboanga city is among the five regions in Mindanao that suffered from flooding and landslides over the weekend, affecting over 60,000 families
On the same day, at least 17 persons have been confirmed dead and 34 others were injured as a passenger bus plunged into ravine in the north Afghanistan's Baghlan province.
The deadly traffic accident took place in Khinjan district due to reckless driving, leaving 17 passengers dead including three children, and two women.
A similar accident claimed one life and injured 15 others in the western Herat province of Afghanistan on July 4.