The death toll from the first storm to batter the disaster-prone Philippines this year has climbed to 40, officials said Sunday, as forecasters warned more heavy rain was on its way.

"Lingling" -- a tropical depression -- has wreaked havoc across the southern island of Mindanao, affecting more than 580,000 people, 161,000 of whom have been displaced and moved to evacuation centres.

Manila's National Disaster Risk Reduction and Management Council upped the number of dead by three from Friday's toll, as the state weather bureau said further "moderate to heavy" rains were expected over large areas of Mindanao.

Public storm warning signals have been hoisted in eight provinces on the island which are expected to be hit by 60 kilometre (37 mile) an hour winds over the next 36 hours.

"Tropical depression Agaton is expected to bring moderate to occasionally heavy rains and thunderstorms over Bohol, Siquijor, Northern Mindanao and the rest of the Caraga region," the bureau said, referring to the storm's local name.

Office of Civil Defence regional director Liza Mazo said a landslide had blocked the national highway in Agusan, slowing the emergency response.

Roughly 20 storms batter the Philippines every year and many areas on Mindanao's eastern coast are still recovering from powerful Typhoon Bopha that left 1,900 dead or missing in December 2012.

The storm is also expected to bring some heavy rains and thunderstorms to the country's central region, where millions remain homeless after Super Typhoon Haiyan cut a swathe of destruction in November.

Haiyan, one of the worst natural disasters to hit the Philippines, left nearly 8,000 dead and missing after it triggered giant tsunami-like waves that swallowed entire coastal communities.

Thousands flee storm, persistent floods in Philippines
Manila (AFP) Jan 17, 2014 - Thousands of people fled rising floods and an approaching storm in a fresh round of evacuations in the Philippines, officials said Friday as the death toll from a week of foul weather rose to 37.

Nearly 13,000 people left their villages along the flooded banks of the Agusan river on the southern island of Mindanao in the past 24 hours, the civil defence office in the region said in an updated report.

"The rains come to this region around this time, but this year has been terrible," John Uayan, an operations official for the government agency, told AFP.

The state weather office said a weather system off the Philippines' east coast has turned into a tropical storm and would hit Mindanao's coast on Saturday, increasing the danger to residents of the already flooded Agusan basin.

The storm looks set to spare the nearby region where Super Typhoon Haiyan left nearly 8,000 people dead or missing and made more than four million people homeless in November -- a rare piece of good news for the disaster-weary Asian nation.

But many in Mindanao were bracing for a fresh wave of appalling weather.

"We expect intense rain over the (Agusan) region starting tonight," forecaster Alczar Aurelio told a news conference.

"The public is being warned about the possibility of landslides and flash floods," Reynaldo Balido, spokesman for the government's National Disaster Risk Reduction and Management Council.

The coastguard expects stormy local waters and has barred ferries from setting sail, Balido told the news conference.

More than 218,000 people are now temporarily housed in schools and other government buildings across the eastern third of Mindanao after a week of bad weather, civil defence officials said Friday.

Some of them have been there since shortly after heavy rains began pounding the region on January 10, they added.

Floods and landslides unleashed by heavy rains killed 18 people in the Agusan basin, including a woman who drowned on Thursday and three gold prospectors whose bodies were pulled from a landslide.

Nineteen other people were killed earlier in the week along Mindanao's east coast, including areas still recovering from Typhoon Bopha that left 1,900 people dead or missing in December 2012, they added.

Two ferries and a cargo vessel ran aground off the central islands of Cebu and Bohol on Wednesday and Thursday, but no casualties were reported and nearly 400 passengers and crew are being transferred to other vessels, the coast guard said.