The storm's movement has slowed slightly but it has also strengthened to pack gusts of 220 kilometres per hour, said Esperanza Cayanan, chief of the government's weather monitoring division.
It was expected to hit the northern edge of the country's main island of Luzon by late this afternoon or evening.
In Taiwan, which is also in the storm's predicted path, authorities warned sailors of strong winds and high waves and evacuated almost 1,000 tourists from an island off the southeast coast.
"This is a very dangerous storm. It is the strongest so far this year," said Rene Paciente, head of the marine weather division.
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More than 2,000 people in Cagayan were being evacuated from coastal villages, said Norma Talosig, regional civil defence chief.
"They have to evacuate to higher ground, not in their village. They are being assisted by the local governments using buses and trucks, even ambulances," she told AFP.
The national civil defence chief, Alexander Pama, said that given the possibility of storm surges of up to two metres, they were taking no chances.
"Even as we speak, our armed forces are already moving... to help in the evacuation. So too are our police forces who are conducting evacuations in their municipalities," he told reporters.
Storm surges - tsunami-like waves generated by powerful typhoons - have become a major concern during storms.
In November 2013 storm surges were the main killers as Super Typhoon Haiyan ravaged the central Philippines, leaving more than 7,350 people dead or missing.
Several hundred people living in a farming hamlet below the restive Bulusan volcano on Luzon have also been evacuated due to the potential for rain to mix with volcanic ash accumulated on its slopes and form deadly, fast-moving mudflows.