The death toll from two storms which battered the Philippines rose to 45 Sunday as several towns remained under water and rain kept falling in northern regions, disaster monitoring officials said.

The rain was caused by a cold front, dragged into the country by Typhoon Melor and Tropical Depression Onyok which hit the Philippines in succession last week.

Floods almost three metres (nine feet) deep covered some riverside areas north of the capital Manila as heavy rain kept falling, civil defence offices said.

"Our home has been flooded up to the waist. It has been flooded for over two days," said Mary Jane Bautista, 35, in the industrial town of Calumpit 50 kilometres (30 miles) north of the capital.

Her family and several others were forced to take refuge on nearby high ground -- in front of a church where their only shelter is the awning over the entrance.

"My husband has to wade through the waters to go home to get supplies. If we need water, he has to go to the faucet in our kitchen," she told AFP, expressing fears the current could wash him away.

"We had some food but it just ran out," she said, complaining that government relief goods had not yet reached her.

Around her the streets had turned into fast-moving rivers, passable only by rowboats and people using inner tubes.

Many low-lying areas north of Manila act as a catchment area for rain in other parts of the main island of Luzon.

"It (the flood) really takes a long time to recede because this is the lowest area," said Glenn Diwa, an officer with the regional disaster council.

Over 54,000 people in the region were huddling in government evacuation centres, she said, adding there was no guarantee they would be home by Christmas, one of the biggest holidays in the largely Catholic nation.

Melor hit the southeast of Luzon on December 14 and moved west across the archipelago.

Even as it departed to the South China Sea, another storm named locally as Onyok hit the southern island of Mindanao and brought more heavy rain.

Almost a week after Melor struck, the death toll was still rising, with the bodies of four dead fishermen washed up in the eastern region of Bicol.

"They left during clear weather. But they were caught by the typhoon on the way home," said Cedric Daep, the region's civil defence chief.

The unregistered vessel did not have a radio or even life vests, he told AFP.

The government weather station said Onyok had dissipated and the weather would improve nationwide by Monday.

The nation of 100 million people is battered by an average of 20 typhoons annually, many of them deadly. In 2013, Super Typhoon Haiyan wiped out entire fishing communities in the central islands, leaving 7,350 people dead or missing.

Recurring flood nightmare in typhoon-battered Philippines
Candaba, Philippines (AFP) Dec 18, 2015 - Tens of thousands of people struggled Friday through waist-deep floods in typhoon-battered farmlands near the Philippine capital, as yet another storm threatened to dump more rain.

Large parts of four farming provinces on the main northern island of Luzon have been submerged in water since Wednesday due to Typhoon Melor, which left at least 27 people dead in its wake.

Hundreds of thousands of people there had yet to recover from Typhoon Koppu, which claimed 54 lives while causing flooding that lasted for more than a week and destroyed vast swathes of rice crops just before harvest in October.

President Benigno Aquino on Friday declared a "state of national calamity" to hasten the government response, his spokesman, Herminio Coloma, told reporters.

Truck driver Roberto Mariano, who has been out of work since Koppu, again found the small bungalow he shared with 15 relatives submerged.

"The floods mean no work and no money for me," the 51-year-old told AFP, trying to keep his balance as he walked through strong flood currents in Candaba, around 50 kilometres (30 miles) north of Manila.

Mariano, who used to earn 500 pesos ($10) driving, was on his way to his parents' house to borrow money to buy rice.

"It's very hard out here. I have to go out because we've run out of food in the house," he said.

Mariano said he had spent the last two nights sleepless, anxiously watching as the waters nearly submerged the children's wooden beds.

- 'We're used to this' -

Flooding was expected to spread to other parts of the country with a tropical depression, locally dubbed Onyok, on course to hit coastal villages on the main southern island of Mindanao late Friday.

In Surigao del Sur province, where Onyok was expected to make landfall first, authorities prepared for possible evacuation and readied trucks and excavators to clear landslide debris, governor Johnny Pimentel told AFP.

"We are prepared for this storm... the biggest threat here is the floods," he said.

While Onyok will hit land about 700 kilometres from the farming regions currently enduring floods, it could still bring rain to those areas, said Esperanza Cayanan, a state weather bureau forecaster.

The weather misery comes a week before Christmas, the most celebrated holiday in the predominantly Catholic nation of 100 million people.

"We should not be in holiday mode," Cayanan told reporters.

In the Candaba town centre, residents with groceries in hand rode small wooden boats and makeshift rafts made from refrigerator doors.

Others showed commitment to their daily routines, eating at roadside canteens waist-deep in flood waters.

"We're used to this, but it doesn't make it any less difficult," said Candelaria Balagtas, a 68-year-old retired policewoman.

The country is ravaged by an average of 20 major storms a year, many of them deadly.

Balagtas said she risked triggering her arthritis by wading through the frigid waters to the market to buy rice and sardines for her daughter after they ran out of food.

"I'm lucky I have my pension, but the people here, their farms were destroyed, the fishermen can't go out to fish," she told AFP.

The islands of the Philippines are often the first major landmass that storms hit after they emerge over the Pacific Ocean.

In November 2013, Super Typhoon Haiyan, one of the strongest storms on record, flattened entire communities in poor farming and fishing communities, leaving 7,350 people dead or missing.