BAYBAY, Leyte (2nd UPDATE) — The death toll from landslides and floods in the Philippines rose to 58 on Wednesday, official tallies showed, as rescuers dug up more bodies with their bare hands in villages crushed by rain-induced avalanches.

Most of the deaths from tropical depression Agaton (international name: Megi) -- the first storm to hit the disaster-prone archipelago this year -- were in the central province of Leyte where a series of landslides devastated communities.

At least 47 people died and 27 were missing after waves of sodden soil smashed into farming settlements around Baybay City over the weekend, local authorities said. Just over 100 people were injured.

Search operations have resumed around Baybay City after the rain stopped, enabling emergency personnel to access hard-hit areas, Mayor Jose Carlos Cari told CNN Philippines.

"In some barangays (villages), we're just doing retrieval," Cari said.

Video from PTV

Three people were also killed in the central province of Negros Oriental and 3 on the main southern island of Mindanao, according to the national disaster agency.

Search operations for survivors in Pilar village -- part of Abuyog municipality in Leyte -- resumed at first light Wednesday, with boats carrying rescuers to the coastal community of around 400 people a day after a landslide pushed most houses into the sea.

"We have 5 casualties, 1 unidentified," Capt. James Mark Ruiz of Abuyog police told AFP.

Around 50 survivors have been rescued from the village, the Bureau of Fire Protection said on Facebook Tuesday.

Raymark Lasco, a radio operator at the Abuyog disaster agency, told AFP that "many people" had died.

"I can't give you exact details... because our operation is ongoing," he said.

National Disaster Risk Reduction and Management Council (NDRRMC) spokesperson Mark Timbal said that as of Wednesday morning, the agency has received reports about the death of 43 people due to the storm.

Of the total, 37 were from search and rescue operations in Leyte province, while six reportedly died due to drowning in Central Visayas and the Davao Region, he said.

"Subject for validation pa rin. Ang injured ay umabot sa 8, at ang missing natin ay umabot na sa 7," Timbal said in a public briefing.

(This is still subject for validation. The injured individuals are 8, and the missing people reached 7 already.)

Rescuers have been using their bare hands and shovels to reach victims buried by the landslides.

A Philippine Coast Guard video shared on Facebook Tuesday showed rescuers carrying a mud-caked woman on a stretcher from one of the devastated villages, while other victims were piggybacked to safety.

The military has joined coast guard, police and fire protection personnel in the search and rescue efforts, which have been hampered by bad weather.

More than 213,000 families or nearly 581,000 people were staying in 348 evacuation centers, based on the NDRRMC's 8 a.m. report.

The affected population are from the Bicol region, Western Visayas, Central and Eastern Visayas, Northern Mindanao, Davao Region, Soccsksargen, Caraga, and the Bangsamoro region.

PORT OPERATIONS SUSPENDED

The NDRRMC said nearly 9,000 passengers, over 2,500 rolling cargoes, 21 vessels and a motorbanca were stuck in ports of Bicol region, Central and Eastern Visayas, and Caraga.

Whipping up seas, Agaton forced dozens of ports to suspend operations and stranded thousands of people at the start of Holy Week, one of the busiest travel periods of the year in the Philippines.

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Agaton came 4 months after super typhoon Odette devastated swaths of the country, killing more than 400 and leaving hundreds of thousands homeless.

• UN: Typhoon Odette destruction 'badly underestimated'

Scientists have long warned that typhoons are strengthening more rapidly as the planet becomes warmer due to climate change.

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The Philippines -- ranked among the most vulnerable nations to its impacts -- is hit by an average of 20 storms every year. In 2013, it was battered by super typhoon Yolanda (international name: Haiyan), which left some 6,300 dead, more than 1,000 missing, and over 28,000 injured.

© Agence France-Presse