Megi was the first cyclone this year to hit the Philippines, an archipelago of more than 7,600 islands that sees an average of 20 tropical storms a year, according to Reuters.
Eighty-six of the casualties were in Baybay, a mountainous area prone to landslides in Leyte province, where 236 people were also injured, the city government said in a report.
Three others drowned in different provinces, while six people were still missing, the national disaster agency said.
"The search, rescue and retrieval operations will continue," a Philippine Army infantry unit in Baybay said on Facebook.
Megi, which made landfall on Sunday with sustained winds of up to 65 kilometers (40 miles) per hour and gusts of up to 80 kph (49 mph), has since dissipated.
The district of Kantagnos had been "greatly devastated", an army engineering and construction battalion on Leyte said on Facebook. "Homes and livelihoods have been damaged, families and individuals are missing and communication have been unstable," said the post.
More than 162,000 displaced residents are sheltering in evacuation centers, while a further 41,000 are living with relatives, government data showed.
Megi's destructive path has revived memories of other deadly storms in the Philippines.
MP/PR