The disaster management official said 16 people were killed in Datu Odin Sinsuat, 10 in Datu Blah Sinsuat, and five in Upi, reports Xinhua news agency.
The casualities may rise further as the rescue operation was ongoing, he added.
Nasrullah Imam, head of the Maguindanao provincial disaster risk reduction and management office, said troops and police were deployed in place to help rescue and evacuate local residents.
Local media reported that the heavy rain was related to the tropical storm Nalgae which is expected to make a landfall on Sunday on the main Luzon island.
According to the Philippine Atmospheric, Geophysical, and Astronomical Services Administration, Nalgae is expected to strengthen into a severe tropical storm on Friday and into a typhoon by Saturday.
The Philippines is one of the most disaster-prone countries globally, mainly due to its location in the Pacific Ring of Fire and Pacific typhoon belt.
On average, the archipelagic country experiences 20 typhoons yearly, some of which are intense and destructive.
In April, the tropical storm Megi dumped rains in central and southern parts of the Philippines, inundating many areas and causing landslides, resulting in over 220 deaths.
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