The Hong Kong Observatory said the track and wind strength of Mangkhut may change under the influence of the terrain of Luzon, but it will still remain a super typhoon after entering the South China Sea from the Pacific Ocean.
Tuguegarao airport terminal was badly damaged, its roof and glass windows shattered by strong wind, which also sent chairs, tables and papers flipping about inside, Lorenzana said.
The Philippine disaster agency said two rescue workers died while trying to free people trapped in a landslide in the mountainous Cordillera region, while police said a body had been found in a river in Manila. No further details were provided.
With a huge raincloud band 560 miles wide, combined with seasonal monsoon rains, the typhoon could bring heavy to intense rain that could set off landslides and flash floods.
It is expected to strike the nation later in the night itself over the extreme northern parts of Philippines, possibly over Luzon.
Most of the rest of the island is under Signal No. 3, meaning it can expect winds of up to 100 kilometers per hour (62 mph) and significant risk to trees, crops and structures.
Staggering winds of 205kph and extreme rainfall caused some structural damage and cut power to more than four million people across the Cagayan province on Luzon Island, around 300km north of Manila.
There was flooding in several provinces and parts of the capital Manila and officials planned to release water from dams, fearing rains could push reservoirs to risky levels.
Commuters courageous the rain and strong winds in Manila, Philippines.
If Typhoon "Ompong" would keep moving at its current speed of 25 kilometers per hour, storm signals may be lowered or removed by Monday, Pagasa Weather Service Chief Esperanza Cayanan said on Saturday during the Command Conference of the National Disaster Risk Reduction and Management Council (NDRRMC).
Tens of thousands of people fled their homes in high-risk areas ahead of the category 5 storm's arrival due to major flooding and landslide risks.
Super typhoon Mangkhut is estimated to be as much as 900 km in diameter and is expected to pose a severe threat to the northern Philippines even if it begins to weaken somewhat before landfall.
There are no immediate deaths reported but Defense Secretary Delfin Lorenzana said officials in northeastern Cagayan province, where the typhoon slammed ashore before dawn, were verifying the drownings of two children.
"The Observatory makes a special appeal to the members of the public to stay away from the shoreline, and not to engage in water sports", said the Hong Kong weather agency.
Typhoon Haiyan left more than 7,300 people dead or missing and displaced over 5 million in the central Philippines in 2013.
Cagayan Gov. Manuel Mamba said by telephone that evacuations of residents from risky coastal villages and island municipalities north of the rice-and corn-producing province of 1.2 million people have started and school classes at all levels have been canceled.
"There has been an aggressive information dissemination to prepare well", he said.