The Philippines raised a fresh weather alert on Monday, days after more than 100 people were killed by the country’s worst storm of the year.

Nearly a million people are still sheltering at evacuation centres or with relatives after losing their homes or being driven out by floodwaters brought by Severe Tropical Storm Trami, which struck from October 22.

The country's weather agency says Tropical Storm Kong-rey will strengthen into a typhoon by Tuesday and pass close to the northern Philippines as early as Wednesday.

The lowest of a five-stage storm alert is in place on the country's northeast coast.

Trami, by contrast, struck some of the country's most populous areas.

The government's disaster agency put the death toll from Trami at 116, with 39 missing.

About 20 big storms and typhoons hit the Philippines or its surrounding waters each year, damaging homes and infrastructure and killing dozens of people. (AFP)