At least three people have died in the Philippines after torrential rain engulfed parts of the main island of Luzon including Manila where neck-deep water swept through homes forcing thousands into emergency shelters.

The National Disaster Risk Reduction and Management Council said mountainous areas to the north of the island were experiencing floods of 1.8 metres (six feet), following persistent rain that began at the weekend.

One person was killed in a storm-related car accident in the northern Apayao mountain region while a child was crushed by a collapsing wall and a man drowned in towns just outside the capital.

Four other people are missing including three washed away by floods and overflowing rivers and a local female tourist who got lost while exploring a cave in the northern resort town of Sagada.

In the capital Manila, a megacity of 12 million people, schools, government offices and the stock exchange were closed as a red alert was raised in the morning -- the highest level of a warning system in which widespread floods are predicted.

"We are trying to save whatever we can. But it was so sudden," J.R Pascual, a father-of-four, told AFP as he tried to take the most important possessions from his home that was flooded up to his waist.

"My neighbour wasn't even able to get his car out."

Pascual lives in a middle-class district of Cavite, a coastal area that is about 15 kilometres (nine miles) from the heart of Manila.

Roads from Cavite and other southern areas into the city were impassable, while some motorists who tried to get through the flooded streets were forced to abandon their cars.

Footage on ABS-CBN television showed people in nearby shanty town communities standing on their corrugated iron roofs, as fast-moving water swept through the windows of their homes.

By early afternoon, the rain had eased and the red alert was lowered for the capital.

One of President Benigno Aquino's top aides said he did not expect a major disaster.

"Compared to other calamities, this is not of the same gravity as the rest. I hope this will be done by tomorrow," Executive Secretary Paquito Ochoa told a nationally televised government disaster briefing.

Nevertheless, thousands of people were believed to be sheltering in evacuation centres or trapped on rooftops while waiting for the water to subside.

Weather forecasters also said more rain was expected to hit Manila and regions to its north in the early evening.

The flooding was due to the normal monsoon being exacerbated by Tropical Storm Trami, which was causing problems despite being more than 500 kilometres (300 miles) from the Philippines, weather forecasters said.

The Southeast Asian archipelago endures about 20 major storms or typhoons annually, generally in the second half of the year and many of them are deadly.

In August last year, 51 people died and two million others were affected when more than a month's worth of rain was dumped in and around Manila in 48 hours.

One of the most devastating storms to hit the capital was in 2009, when Tropical Storm Ketsana led to 80 percent of the capital being submerged.

It was immediately followed by Tropical Storm Parma, and more than 1,100 people died in the back-to-back disasters.

Chaotic urban planning is widely blamed for exacerbating the impacts of storms in Manila and other parts of the country, which has had to deal with massive population growth over the past generation.

Widespread deforestation, the conversion of wetlands to farms or cities, and the clogging up of natural drainage systems with garbage are some of the factors that worsen floods.

The deadliest storm in the world last year occurred in the Philippines, when Typhoon Bopha left more than 1,000 dead and 800 others missing in the south of the country.

The southern areas are usually spared from the typhoons, and communities there were unprepared for Bopha.