It was located about 800 kilometers (500 miles) away in the Pacific with sustained winds of 265 kilometers (165 miles) per hour and gusts of up to 325 kph (201 mph).
The country's deadliest on record is Super Typhoon Haiyan, which left more than 7,350 people dead or missing across the central Philippines in November 2013.
Ten million people are in the path of the storm, along with millions more in coastal areas of southern China.
It's expected to be 179 nautical miles (331.5 kilometers) off Kaohsiung in southern Taiwan on September 15 before heading to Hong Kong, according to the US agency.
Up to 43.3 million people from Guam, Northern Mariana Islands, the Philippines and China could be affected by the super typhoon, according to the Global Disaster Alert and Coordination System.
With a massive raincloud band 900 kilometres wide, combined with seasonal monsoon rains, the typhoon could bring heavy to intense rains that could set off landslides and flash floods, government forecasters said.
The Joint Typhoon Warning Centre in Hawaii categorized the storm as a super typhoon with powerful winds and gusts.
The Meteorological and Geophysical Bureau (SMG) told Macau News Agency (MNA) that current predictions indicate Typhoon Signal No.8 or No.10 could be hoisted between September 15 (Saturday) night and September 16 (Sunday) due to Typhoon Mangkhut.
"I worry especially for houses made of light materials", said Marilou Cayco, governor of Batanes, a chain of seven remote islands 240 km (149 miles) off the mainland where she said up to 3,000 families could be "battered".
While Mangkhut is not expected to cause similar destruction, Philippines authorities warned it could cause around $250 million in damages to rice and corn crops in the region. He said classes would be suspended and offices, except those involved in rescue and relief work, had been advised to close on Friday.
The storm, named after a fruit in Thailand, is forecast by the USA military's Joint Typhoon Warning Center to bring top winds of 145 knots (268 kilometers per hour) with maximum gusts of 175 knots.
Across the north on Thursday, residents covered glass windows with wooden boards, strengthened houses with rope and braces and moved fishing boats to safety.
About 20 cyclones pass through the disaster-prone country each year. About 80 per cent of the United States territory was without power but it was restored by Thursday morning.