Super Typhoon Doksuri was packing maximum sustained winds of 185 kilometres per hour (115 miles per hour) as it headed towards the northern tip of the main island of Luzon.
The storm, which is called "Egay" in the Philippines, was expected to make landfall or pass very close to the lightly populated Babuyan islands or northeastern Cagayan province by Wednesday, the agency said in its latest bulletin at 0300 GMT.
It would then move towards Taiwan and southeastern China.
Coastal communities in northwestern and northeastern Cagayan province had been ordered to evacuate their homes in anticipation of storm surges reaching, or even exceeding, three metres (10 feet).
Three of the five Babuyan islands are inhabited, with a population of around 20,000 people.
Local disaster official Charles Castillejos said people living near the shores of those islands had been ordered to go inland, while fishermen had been told to get their boats out of the water.
"We sent the police to convince the hard-headed ones who refuse to evacuate," Castillejos told AFP.
Science and technology secretary Renato Solidum said people needed to be prepared for the typhoon because "things happen fast".
"We need to remind our people the importance of readiness against storm surges, strong winds and also possible floods," Solidum told reporters.
Some farmers in the northern province of Isabela, bordering Cagayan, were seen leading their livestock to safety ahead of the storm.
"Those living on coastal areas have been moved to higher ground," Isabela provincial disaster officer Constante Foronda told local radio station DZBB.
"Our water search and rescue teams are now deployed in those areas most likely to be affected," Foronda said.
- Flooding, landslides 'highly likely' -
The Philippines is hit by an average of 20 major storms each year that kill hundreds of people and keep vast regions in perpetual poverty.
Scientists have warned that such storms, which also kill livestock and destroy key infrastructure, are becoming more powerful as the world gets warmer because of climate change.
Boats, including wooden outriggers and passenger ferries that provide transport between islands, have been ordered to shore in Luzon and central islands due to gale warnings, stranding more than 11,000 people, the Philippine Coast Guard said.
By midday Wednesday, the storm was expected to have dumped more than 200 millimetres (7.9 inches) of rain on the islands and the northern portion of Cagayan, including Babuyan islands, as well as Ilocos Norte and Ilocos Sur provinces.
Heavy rain was also expected across the mountainous northern provinces in the coming days, with flooding and landslides "highly likely", the weather agency said.
Cagayan provincial disaster officer Ruelie Rapsing told DZBB that emergency food packs had been stored in warehouses.
"The province has been on red alert status since Saturday and all evacuation centres, emergency operation centres of each town, and incident management teams are activated," he said.
"Cagayanons are used to this."
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