The Philippines sharply revised the death toll from a tropical storm ravaging the country downward on Saturday, saying only 45 people had been killed -- correcting the earlier reported toll of 72.

Civil defence officials acknowledged rescue teams sent to the country's flood-swamped south on Friday had erred in their reporting, leading to some deaths being tallied twice.

"When we consolidated the reports at 6:00 am today we realised there were only 40 dead, 31 injured and 15 missing," Naguib Sinarimbo, spokesman and civil defence chief for the southern region told AFP.

National civil defence chief Rafaelito Alejandro also confirmed the lower figure at a news conference in Manila, saying 40 bodies were recovered from the disaster in the southern region of Mindanao.

Tropical Storm Nalgae killed five other people elsewhere in the country, Alejandro added.

Earlier Saturday the civil defence office reported 72 dead, 14 missing and 33 injured.

Alejandro told reporters the death toll was reduced after local officials conducted a "validation" of the reports.

Nalgae was ripping across the main Philippine island of Luzon on Saturday with winds of 95 kilometres (59 miles) an hour after a pre-dawn landfall.