Typhoon Utor made landfall in the north of the main island of Luzon early on Monday, bringing winds of up to 124 mph and torrential rain.
Power lines were brought down in some places and ferries were suspended, stranding thousands of passengers.
Typhoon Utor is expected to remain in the northern Philippines for most of Monday before sweeping out to sea.
It is then expected to move across the South China Sea towards southern China.
Heavy rain hit the capital, Manila, where some schools were closed, but there were no reports of major flooding.
A number of domestic flights were also cancelled.
The missing fishermen all come from Catanduanes, an island province off Luzon’s east coast.
Officials said they hoped the men had taken shelter in nearby islands.
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