The Huey helicopter went down in Agusan del Sur on the island of Mindanao, where it was conducting a humanitarian disaster response mission, the military said.
Six bodies of the crew were recovered and an investigation was underway.
The crash took place before noon about 270 km from the island of Cebu, the worst-hit region, where local authorities said 39 people had been killed by drowning or falling debris.
One person was reported dead on the neighbouring island of Bohol.
Although Kalmaegi, locally named Tino, has gradually lost strength since making landfall early on Tuesday, it continued to lash the country with winds of 120 kph and gusts of 165 kph as it swept across the Visayas islands headed for northern Palawan and towards the South China Sea.
Tens of thousands were evacuated across the Visayas region, including parts of southern Luzon and northern Mindanao, ahead of a storm that submerged homes and caused widespread flooding.
Cebu provincial information officer Ainjeliz Orong said the number of casualties in the province had jumped suddenly, from three reported earlier in the day, as rescue operations were underway and information had just started to come through.
“Search and rescue efforts continue and there are missing and unaccounted individuals,” Orong said by phone.
Floods in Cebu City had subsided late on Tuesday but power was still out in many places and telecommunications services were intermittent, a Reuters journalist said.
Verified videos circulating on social media showed cars and streets under water, with some vehicles carried away in the flow.
After the flood receded in one area of Cebu City, cars shifted by fast-flowing water were left piled up on top of each other, some overturned.
“We were really anxious because the longer the rains continued, the higher the floodwaters rose,” said John Patajo, a housekeeper in the area.
“When the waters rose, we went to our second floor. Yet, the waters kept rising so we decided to head up to our roof.”
The typhoon was expected to leave the Philippines late on Wednesday or early Thursday.
More than 300 flights to and from the affected areas were cancelled on Tuesday, while boats at sea were advised to return.
The Vietnamese government on Tuesday said that it was preparing for the worst-case scenario as it braced for the impact of Kalmaegi.
The typhoon is forecast to make landfall on Thursday night in Vietnam’s central regions, which have already suffered heavy floods that killed at least 40 people and left six others missing over the past week.
“This is a very strong typhoon, which continues to strengthen,” the government said. (Reuters)
