Heavy flooding inundated the Philippines' capital on Tuesday, forcing tens of thousands of people to flee and schools and government offices to shut, while a fresh storm brewed off the coast.

At least six people have died and another six remain missing after Tropical Storm Wipha skirted the country on Friday, according to the National Disaster Risk Reduction and Management Council.

Many neighbourhoods in Manila woke to find calf-deep pools of floodwater on Tuesday after an overnight downpour swelled the Marikina River.

More than 23,000 people living along the riverbank were evacuated from their homes overnight and moved to schools, village halls and covered courtyards.

About 47,000 more were evacuated from across the capital's Quezon, Pasig and Caloocan areas, as well as from the main government district.

"Usually, these people are from low-lying areas like beside creeks," said Wilmer Tan of the Marikina rescue office, who said the river had reached 18 metres in height.

As floodwaters began receding in Manila by Tuesday afternoon, the national weather service said a low-pressure area off the country's east coast had developed into a tropical depression.

While not expected to make landfall, the depression would bring continued heavy rain through the end of the week, the agency said.

In Vietnam, Wipha hit the northern provinces of Ninh Binh and Thanh Hoa early on Tuesday with wind speeds of up to 74 kilometres per hour, slowing from around 100kph on its approach, the national weather forecasting agency said.

Heavy rains of up to 50 centimetres were forecast to continue until Wednesday morning, and authorities warned people to watch out for landslides in mountainous areas and flooding in urban areas.

Around 350,000 soldiers were put on standby. (AFP/Reuters)