Thousands of people living in coastal areas of the Philippines were preparing on Monday to evacuate as the first major storm of the rainy season barrelled towards the archipelago.

Tropical Storm Rammasun is expected to hit fishing communities in the eastern Philippines late Tuesday and then bring heavy rain to Manila and other heavily populated northern areas, civil defence officials said.

The Philippines is hit by about 20 major storms a year, many of them deadly, and Rammasun will be the first to make landfall since the rainy season began last month.

Authorities said they were taking every precaution to avoid fatalities, after Super Typhoon Haiyan left about 7,300 people dead or missing when it tore across the central Philippines in November last year.

"We are already warning the public to be on alert for possible effects of the weather disturbance: landslides, flash floods, strong rains and winds," said Alexander Pama, head of the National Disaster Risk Reduction and Management Council.

Miguel Villafuerte, governor of Camarines Sur province in southern Luzon which is expected to be hit hard by the storm, said many people in vulnerable areas were already being urged to flee.

"We are extra-cautious because of what happened with Yolanda last year," he said, using the local name for Haiyan.

The disaster management council said it had already alerted over 1,300 villages susceptible to floods or landslides they were in Ramassun's direct path and residents should be prepared to shelter in evacuation centres.

The second level of a three-step storm alert has been raised over the Bicol archipelago southeast of Manila, where the storm is expected to first hit. Classes on all levels have already been suspended.

Heavy rain is also expected to fall over the central islands that bore the brunt of Haiyan and where thousands of people are still living in tents or other makeshift evacuation centres.

Storm alerts have also been hoisted for the more than 12 million people in Manila, with some classes having already been suspended.

The new storm is expected to bring 7.5 to 15 millimetres (0.3 to 0.6 inches) of rainfall per hour, the disaster council said.

Council spokeswoman Mina Marasigan warned that the storm could become even more powerful as it moves across the sea.

She said there were concerns it might bring rainfall comparable to Typhoon Xangsane in 2006, which killed more than 200 people and displaced nearly two million due largely to widespread and heavy flooding.