More than 12,700 residents from 12 towns in the province of Surigao del Sur province, 835 kilometres south of Manila, were ordered to evacuate homes in low-lying areas and near the coast.
Provincial Governor Ayec Pimentel said more people were expected to be evacuated ahead of tropical storm Dujuan's projected landfall on Sunday afternoon along the coast of Surigao.
Dujuan was packing maximum sustained winds of 75 kilometres per hour (kph) and gusts of up to 90 kph, the weather bureau said in its bulletin.
The storm was moving eastward at 15 kph, and expected to bring intense rains over Surigao and nearby provinces over the weekend before weakening into a tropical depression, the bureau added.
"Scattered to widespread flooding, including flash floods, and rain-induced landslides are likely during heavy or prolonged rainfall,” the bulletin said.
River channels may also swell, causing more floods in other areas, it added.
The Philippines is hit by an average of 20 tropical cyclones every year.
The strongest typhoon to hit the country was Typhoon Haiyan, which killed more than 6,300 people and displaced more than 4 million in November 2013. - dpa