Forecaster Meno Mendoza said Mangkhut's strong winds could whip up storm surges while heavy rain could trigger landslides and floods.
Mangkhut, classified by the Hong Kong Observatory as a super typhoon, is now forecast to pack maximum winds of 250 kilometers (155 miles) per hour by Friday before gradually weakening.
Cathay Pacific Airways Ltd. encouraged passengers travelling this weekend to and from Hong Kong to re-book and the airline will waive the fees.
Cagayan Governor Manuel Mamba said by telephone that northern coastal and island villages in the typhoon's projected path will begin evacuating residents on Thursday ahead of the expected onslaught.
Mangkhut, locally known as super typhoon Ompong, has already passed the US territory of Guam, where it caused widespread flooding and power outages.
The storm, named after a fruit in Thailand, is forecast by the U.S. military's Joint Typhoon Warning Center to bring top winds of 145 knots (268 kilometers per hour) with maximum gusts of 175 knots.
Duterte issued the order during the command conference with weather, disaster, and other government officials at the National Disaster Risk Reduction and Management Council (NDRRMC) operations center in Camp Aguinaldo, Quezon City. Government agencies were conducting damage assessments and beginning to clear roads, according to the Pacific Daily News.
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On Guam, the typhoon knocked down houses, power lines and trees, with around 88 per cent of the island having electricity by Thursday morning.
In 2016, a super typhoon lashed the southern section of Cagayan, destroying tens of thousands of houses.
"I'm stressing that this one is very different".
The strongest typhoon to hit the Philippines this year is threatening the farmlands in Northern Luzon just before the rice and corn harvest. In its September 11 update, weather bureau PAGASA said Ompong is expected to be within PAR by Wednesday afternoon and remain until Saturday.
Last year, at least eight people died in Macau as a result of Typhoon Hato, the strongest storm to hit the city in over five decades, which also caused widespread flooding and damage to property.
Medical and emergency response teams were on stand by, heavy equipment mobilised and more than 1.7 billion pesos ($31.45 million) of relief goods prepared as Mangkhut, known locally as Ompong, edged towards the storm-prone nation on its way towards southern China and northern Vietnam.