Nearly 13,000 people left their villages along the flooded banks of the Agusan river on the southern island of Mindanao in the past 24 hours, the civil defence office in the region said in an updated report.
"The rains come to this region around this time, but this year has been terrible," John Uayan, an operations official for the government agency said.
The state weather office said a weather system off the Philippines' east coast has turned into a tropical storm and would hit Mindanao's coast on Saturday, increasing the danger to residents of the already flooded Agusan basin.
But many in Mindanao were bracing for a fresh wave of appalling weather.
"We expect intense rain over the (Agusan) region starting tonight," forecaster Alczar Aurelio told a news conference.
"The public is being warned about the possibility of landslides and flash floods," Reynaldo Balido, spokesman for the government's National Disaster Risk Reduction and Management Council.
The coastguard expects stormy local waters and has barred ferries from setting sail, Balido told the news conference.
Some of them have been there since shortly after heavy rains began pounding the region on January 10, they added.
Floods and landslides unleashed by heavy rains killed 18 people in the Agusan basin, including a woman who drowned on Thursday and three gold prospectors whose bodies were pulled from a landslide.
Nineteen other people were killed earlier in the week along Mindanao's east coast, including areas still recovering from Typhoon Bopha that left 1,900 people dead or missing in December 2012, they added.
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