Slum dwellers in the Philippine capital rummaged through their flattened homes Thursday as villagers on remote farms battled floods, two days after a monster typhoon killed at least 39 people.

Authorities warned the death toll from Typhoon Nesat would continue to climb, with dozens of people still missing and more accidents likely as tens of thousands of others struggled with the storm's aftermath.

"Rescuers are using rubber boats and canoes to help those in areas still flooded," Office of Civil Defence chief Benito Ramos told AFP.

"Many are marooned on rooftops, mostly menfolk who refused to join pre-emptive evacuations so they could guard their homes."

Ramos said many of the missing were fishermen who set sail ahead of the storm despite warnings to remain on land.

"We are just praying that we will find them still alive, but realistically speaking, the number of deaths may still rise," he said.

Four more people were reported dead on Thursday evening, bringing the official death toll to 39. However 14 fishermen were found safely, reducing the number of missing to 31.

The Philippines endures an average of 20 storms annually, many of them deadly, but Nesat was one of the worst of the year largely due to an enormous rain band that pummelled virtually all of the main island of Luzon.

Nesat was approaching southern China on Thursday, forcing Hong Kong authorities to order a lockdown in the Chinese territory with the closure of financial markets, schools and transport services.

Manila had been brought to a similar standstill on Tuesday as rain flooded large parts of the Philippine capital and storm surges smashed sea walls protecting the city's historic bayside area.

Officials said it would take many days to clear fallen trees, billboards and other debris across the city.

In one shantytown district, flooding remained thigh-deep, forcing the elderly to simply wait for the waters to recede.

"We just have to bear it because we don't have anywhere else to go," 69-year-old widow Lorena De Lima said from the second floor of an abandoned factory where she makes her home.

In Luzon's vast agricultural plains that stretch hundreds of kilometres (miles) to the north of Manila, farmers struggled to deal with the destruction of rice that was primed for harvest.

Television news broadcasts showed aerial footage of high water covering large areas of the northern provinces of Bulacan, Nueva Ecija and Pampanga, where many of the country's large rice producing plains are located.

Many of those areas remained without power or cut off because highways and farms had been turned into virtual rivers.

Nearly 170,000 people were inside evacuation centres across Luzon, according to the government's disaster relief agency.

Amid the clean-up operation, civil defence chief Ramos warned Typhoon Nalgae, bearing gusts of 140 kilometres (miles) per hour, could hit the country by Saturday, bringing renewed misery to the northern part of Luzon.

"Those people in evacuation centres should just stay in evacuation centres because they might be hit again," Ramos told AFP.

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