Strong rain since Monday caused a landslide in the town of Pagbilao in Quezon province, about 145 kilometers (90 miles) south of Manila, resulting in the two fatalities, the Office of Civil Defense said.
A protective dyke collapsed near the town of Naujan in Oriental Mindoro island province also south of the capital, causing floods that displaced more than 47,000 people, it said.
Some 15,000 people were also relocated to higher ground in Quezon. There was also flooding and reports of scattered landslides in the eastern province of Camarines Norte.
Search and rescue teams have been deployed to the affected areas and the military's Southern Luzon Command has dispatched trucks for the relief effort.
Also, at least two helicopters and several inflatable boats were sent to support rescue and relief efforts.
The state weather bureau had earlier forecast more rain to hit the area this week.