A storm unleashed pounding rains that flooded many northern Philippine areas overnight into Monday, prompting authorities to suspend classes and government work in the capital region and warn thousands of residents to prepare to evacuate from flood-prone villages along a key river.

Tropical Storm Yagi was blowing 115 kilometres (71 miles) northeast of Infanta town in Quezon province, southeast of Manila, on Monday with sustained winds of up to 75 kilometres (47 miles) per hour and gusts of up to 90 kph (56 mph), according to the weather bureau.

The storm, locally called Enteng, was moving northwestward at 15 kph (9 mph) near the eastern coast of the main northern region of Luzon, where the weather bureau warned of possible flash floods and landslides in mountainous provinces.

Two residents died amid the stormy weather in Naga city in eastern Camarines Sur province, where floodwaters swamped several communities, police said. Authorities were verifying if the deaths, including one caused by electrocution, were weather-related.

Storm warnings were raised in a large swath of Luzon, the country's most populous region, including in metropolitan Manila, where schools at all levels and most government work were suspended due to the stormy weather.

Along the crowded banks of Marikina River in the eastern fringes of the capital, a siren was sounded in the morning to warn thousands of residents to brace for evacuation in case the river water continues to rise and overflows due to heavy rains.

In Northern Samar province, coast guard personnel used rubber boats and rope to evacuate 40 villagers on Sunday in two villages that were engulfed in waist- to chest-high floods, the coast guard said.

Sea travel was temporarily halted in several ports affected by the storm, stranding about 2,200 ferry passengers and cargo workers, and several dozen domestic flights were suspended due to the stormy weather.

Downpours have also caused water to rise to near-spilling level in Ipo dam in Bulacan province, north of Manila, prompting authorities to schedule a release of a minimal amount of water later Monday that they say would not endanger villages downstream.

About 20 typhoons and storms batter the Philippines each year. The archipelago lies in the “Pacific Ring of Fire,” a region along most of the Pacific Ocean rim where many volcanic eruptions and earthquakes occur, making the Southeast Asian nation one of the world's most disaster-prone.

In 2013, Typhoon Haiyan, one of the strongest recorded tropical cyclones in the world, left more than 7,300 people dead or missing, flattened entire villages, swept ships inland and displaced more than 5 million people in the central Philippines.