Philippines President Benigno Aquino has declared a national calamity after Typhoon Washi slammed into southern Mindanao island at the weekend.
Flood waters and landslides have caused extensive damage to crops, infrastructure, and more than 10,000 houses.
Habitat for Humanity plans to provide shelter assistance to at least 5,000 families over the next three months, primarily in the cities of Iligan and Cagayan de Oro.
Support will include the provision of tools and clean-up kits, and latrine construction.
Ian Pearce, Habitat for Humanity Programme Manager said it was essential for families caught up in natural disasters to move back into permanent homes "as soon as possible".
"Homes are the centre of our lives, providing a place to generate a livelihood, giving children a safe, secure, healthy place to grow up and a place to study," he said.
"Without decent homes families who are already vulnerable risk being plunged into abject poverty for generations to come."
He warned that any delays to the provision of new homes would affect children's education, as emergency shelters tend to be set up in schools.
"This makes communities even more vulnerable to future disasters, so it is of the utmost importance that we help people back into decent homes," he said.
Christian Aid has already allocated £50,000 to its response but has launched an emergency appeal to assist even more people.
Its partners are distributing emergency supplies to 950 families in the Cagayan de Oro area. In Iligan, another 1,000 families who have lost their means of earning an income will receive cash transfers to enable them to buy food in local markets.
Alwynn Javier, who is co-ordinating Christian Aid's response from Manila, said: "Christian Aid has worked with local partners in this area before and they are well placed to identify the most vulnerable members of the affected communities so they can be targeted first for emergency assistance."
OMF International said its main partner church in the Philippines is helping in the clean-up operation despite the fact that two-thirds of the congregation have been affected by the floods.
Its partner in the region, Mark Chapman, said the emergency services had been "overwhelmed" by the fatalities and that in some cases, entire families had been killed.
"Pray that more people will be found alive despite the odds and that those needing medical attention will receive the help they need," he said.