The death toll rose from four a day after the storm brought heavy rain to the Bicol and Eastern Visayas regions, causing massive flooding and landslides.
Luzon is the largest island in the Philippines and home to some 53 million people.
Typhoon Trami has already snarled travel in the world's third-biggest economy, with bullet train services suspended, more than 1,000 flights cancelled and Tokyo's evening train services scrapped.
Television footage showed cars in Okinawa island flipped over by the strength of the wind.
The airport’s operator said it will close two runways from 11 am local time on Sunday to 6 am on Monday, halting all takeoffs and landings.
At least 386 flights were cancelled mainly in western Japan.
The village of Ucab in the picturesque Cordillera region was hit by one of 50 landslides triggered by heavy rains brought by Typhoon Mangkhut.
Mangkhut had shut the city all day Sunday after the Observatory gave the storm its highest warning signal.
More than 2.4 million people have been relocated and nearly 50,000 fishing boats were called back to port.
The world’s largest gambling hub suspended gaming operations at all its casinos as Typhoon Mangkhut ripped through the region.
Mangkhut has weakened since blasting into the Philippine coast but was packing sustained winds hurtled toward China's heavily populated southern coast.
Mangkhut’s structure will be ripped by wind shear, weakening its top winds as it approaches the coast to Hong Kong’s west.
Mangkhut entered the Philippines as a super typhoon in the early hours, and sent winds and rains across Luzon, home to about half the country's 105 million people.
Airlines across the region cancelled more than 100 flights on Saturday as Super Typhoon Mangkhut slammed into the Philippines.
The worst storm surge comes in with a hurricane's eye, and it arrives 'with a lot of debris to batter you, and it's not particularly survivable'.
The civil defence office in Manila said towns and cities on Mangkhut's path are preparing government buildings as evacuation centres, stockpiling food and other emergency rations.
600 flights were cancelled along with ferries connecting ports in western Japan.
Japan has been hit by various extreme weather since the beginning of July with record-breaking heat and devastating floods that killed more than 200 people.
The cancellation was announced by Britain's embassy in Japan and the Ministry of Defence in Tokyo.
The typhoon will bring heavy rain across the main island of Honshu, with 400 mm (15 inches) possible in the region around Tokyo in the 24 hours to Sunday noon.
Typhoon Jongdari is currently packing winds of nearly 200 kilometres (125 miles) an hour, forecast to hit the country's main island on Saturday night, Japan's Meteorological Agency said.
The aircraft, which will eventually replace the Typhoon fighter jet, will be developed and built by partners BAE Systems, Rolls-Royce and Leonardo, the source said.
The Tokyo metropolitan government has unveiled its first estimate of the Japanese capital's vulnerability to damage from typhoon-related high tidal waves, as risks of storm damage continue to increase globally.