A new storm was threatening to dump heavy rain on the southern Philippines on Friday, as people in northern farming regions battled floods from deadly Typhoon Melor, authorities said.

A tropical depression, locally named "Onyok", was heading for the southern island of Mindanao as Melor moved further out to the South China Sea after claiming at least 20 lives, the government weather bureau reported Thursday.

Melor tore in from the Pacific Ocean and hit the eastern Philippines on Monday, then caused major flooding across the central and northern regions of the archipelago throughout the week.

Although the typhoon left the Philippines on Wednesday, floodwaters about a metre (three feet) deep still covered farming regions about an hour's drive north of Manila, the national capital.

Local disaster management officer Angie Blanco said these floods were expected to rise further as waters from other parts of the main island of Luzon flowed into the floodplain.

"Maybe tonight, it will hit four to five feet," Blanco told AFP.

"But people are not leaving unless they are forced to do so. They are used to this situation."

In the riverside town of Macabebe, about 42 kilometres (26 miles) north of Manila, men with rolled up trousers and women holding up their skirts waded through knee-deep waters, carrying sacks of groceries and bottles of drinking water on their shoulders.

"Their houses are built high so they don't think they need to evacuate but disaster control personnel are on standby if the waters rise further," Blanco said.

On the mainly rural southern island of Mindanao, which will be hit by Onyok, preparations were underway for the depression which is forecast to hit on Friday.

Although Onyok is only a tropical depression, it is forecast to bring heavy rain to areas not used to fierce weather.

The Philippines is hit with about 20 major storms a year, many of them deadly, but they normally strike north of Mindanao.

But some of the storms have in recent years tracked further south, catching residents unprepared with horrific consequences.

Tropical Storm Washi claimed more than 1,200 lives after striking Mindanao in December 2011, then Typhoon Bopha left at least 1,900 dead and missing in the same region a year later.

Government agencies in the Mindanao regions in Onyok's path said they were making preparations.

"We will do pre-emptive evacuation and forced evacuation if necessary," Amado Posa, the area's disaster management operations officer, told AFP.

Other preparations include identifying vulnerable areas, designating evacuation centres and pre-positioning heavy equipment and food supplies, he said.