The guerillas attacked the army relief convoy early on Friday, wounding two soldiers, a disaster management official said.
"An army convoy was ambushed after delivering relief goods in typhoon-hit areas," said Alexander Pama of the National Disaster Risk Reduction and Management Council.
An army spokesman blamed Maoist-led rebels for the attack.
The communist New People`s Army has waged a guerrilla campaign in the region for more than four decades, and the attack came just five days ahead of a unilateral ceasefire declared by the rebels.
Reuters could not immediately reach a rebel spokesman for comment.
Media reported 41 people had been killed in the storm by falling trees, drowning and electrocution, as well as being buried in landslides.
Four people were missing, with 20 injured and nearly 750,000 moved to evacuation centers. About a third are still in shelter areas, expecting to spend Christmas next week homeless and without power.
More than 935 million pesos ($19.71 million) worth of infrastructure and farmland were devastated as up to 300 mm (12 inches) of rain inundated rice paddies on the main island of Luzon and strong winds uprooted trees, the disaster agency said.
Domestic flights and ferry services have resumed but some schools stayed shut. Communications and power returned to some areas while roads have been cleared of debris.
Officials said another storm could bring heavy rain late on Friday to the southern island of Mindanao.
The Philippines is hit by about 20 typhoons a year. In 2013, typhoon Haiyan killed more than 6,300 people and left 1.4 million homeless.
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