The two were identified as Sagapo Cabigding, 63, of Glan in Sarangani and Rolando Mata, 40, from General Santos City.
A certain Rani Pregoner was also reported missing.
Meanwhile, 19 fishermen were rescued from the villages of Ostigue, Baybay, Big Margus and Kalambiga in Glan, the NDRRMC said.
In Sultan Kudarat, 2,460 families were affected from villages of Obial, Sta. Clara, Hinalaan, Himulan and Kalamansig due to heavy rains.
Twenty-three of these families were already evacuated to higher grounds, it added.
Two national bridges remained impassable in Sultan Kudarat as of NDRRMC’s 9p.m. update.
In Bukidnon, the villages of Cabangahan, Bangkud, Adlayan and Linabo in Malaybalay also experienced knee level flashfloods brought by the shallow low pressure area.
Evacuation for residents was being readied if needed, the NDRRMC said.
With moderate forecast rainfall for the next 24 hours, watercourses likely to be affected are rivers, tributaries and streams in Maguindanao, Basilan, Sulu and Lanao del Sur, Misamis Oriental, Misamis Occidental, Lanao del Norte, Bukidnon, Surigao del Sur, Surigao del Norte, Dinagat Island, Agusan del Sur, Agusan del Norte,Zamboanga provinces and Davao region, the NDRRMC said in its flood advisory.
As of 5p.m., the shallow low pressure area causing the rains in Mindanao was seen 110 kilometers southwest of Cotabato City.
Mindanao and Visayas will have mostly cloudy skies with scattered rainshowers and thunderstorms becoming cloudy with widespread rains over Davao provinces, Southern Mindanao and Zamboanga provinces which may trigger flashfloods and landslides, the Philippine Atmospheric Geophysical and Astronomical Services Administration said.
Local disaster risk reduction and management council are monitoring affected villages and continuously assisting the affected families.