Seventy houses in Samar were destroyed and in nearby Romblon province, 20 homes were swept away.
The storm also caused heavy disruption to transport and according to the National Disaster Coordinating Council, nearly 10,000 people were stranded aboard hundreds of ferries and motor boats, which were ordered to stay in port for safety.
More than 60 domestic flights were also cancelled.
In Quezon province, located about 110km southeast of the capital Manila, a tornado struck a fishing boat that had taken cover in a cove, killing four fishermen and injuring two others.
|School classes were cancelled throughout the region because of the storms [EPA]
Pepito Reyes, mayor of Perez township, said the six were sleeping on the boat when the tornado hit.
"The twister lifted the boat and hurled it back into the waters, pinning and drowning the fishermen,'' Reyes told The Associated Press.
Elsewhere waves and strong winds whipped up by the storm caused a passenger boat to capsize off central Mactan Island.
Philippine coast guard ships rescued all 14 aboard the boat, officials said.
Gilbert Teodoro, the country's defence secretary, warned villagers living in flood- and landslide-prone areas to be vigilant and start moving to shelters if they feel threatened.
The storm, internationally named Nangka, is the sixth to hit the Philippines this year.
About 20 typhoons and storms lash the archipelago annually.