Rai was the 15th and deadliest typhoon to hit the Southeast Asian nation this year.
Reported deaths had reached 405 mostly due to drowning, fallen trees and landslides, national disaster agency chief Ricardo Jalad told a news conference on Friday. He said 82 were missing and 1147 injured.
More than 530,000 houses were damaged, one third of which were totally wrecked, while damage to infrastructure and agriculture was estimated at 23.4 billion pesos ($A630 million), Jalad said.
The typhoon affected nearly 4.5 million people, including about 500,000 sheltering in evacuation centres, government data showed.
It made landfall as a category 5 typhoon on December 16, and left a trail of destruction in the provinces of Bohol, Cebu, and Surigao del Norte, including the holiday island of Siargao, and the Dinagat Islands.
In central Philippine provinces, disaster and government officials have been grappling with inadequate relief supplies for thousands of residents still without power and water.
"It caused massive destruction and it was like a bomb was dropped in northern Bohol," Anthony Damalerio, chief of Bohol province's disaster agency, told Reuters.
A popular dive spot, Bohol reported 109 deaths and is seeking shelter kits, food and water, Damalerio said.
"Our problem is shelter, those who lost roofs, especially now that this is rainy season in the province," Surigao del Norte Governor Francisco Matugas told ANC news channel.
Rai's swath of destruction revived memories of typhoon Haiyan, one of the most powerful tropical cyclones ever recorded, which killed 6300 people in the Philippines in 2013.
