More than 300,000 people remain in evacuation camps, with more than 200,000 others sheltering in the homes of relatives or friends.
Some survivors have likened Typhoon Rai to Super Typhoon Haiyan, which left 7,300 people dead or missing across the central Philippines in 2013 and remains the country's deadliest on record.
The archipelago gets hit by an average of 20 cyclones each year.
As the government rushed to bring food, water and clothing to devastated areas, a new threat appeared in recent days with at least 140 people falling ill from suspected contaminated water.
Eighty people were taken ill with acute gastroenteritis in the southern province of Dinagat Islands, while 54 people are being treated for diarrhoea in hospital on the neighbouring tourist island of Siargao, health undersecretary Maria Rosario Vergeire said.
The central city of Cebu reported 16 diarrhoea cases, she told reporters.
"We all know these areas suffered water interruption. Some areas still have tap water but pipes have been damaged and so there is a possibility of contamination," Vergeire said.
Vergeire said the typhoon also spoiled more than 4,000 doses of coronavirus vaccines and damaged 141 hospitals and clinics, only 30 of which have resumed full operations.