Mark Timbal, spokesperson for the National Disaster Risk Reduction and Management Council (NDRRMC), said 12 fishermen from Catanduanes, an island province in the Bicol region, were reported missing, reports Xinhua news agency.
The Philippine Coast Guard (PCG) also reported that one person went missing after a yacht capsized off Bauan town in Batangas province, south of Manila.
The seven other crew members of the yacht were rescued, the PCG said.
Typhoon Molave made its first landfall in Tabaco City, south of Manila, on Sunday evening.
In a report, the NDRRMC said there were no immediate reports of deaths from the typhoon.
However, the agency said the typhoon, packing sustained winds of 125 km per hour and gusts of up to 150 km per hour, has affected at least 4,316 families so far in at least four regions south of Manila and the Cordillera Administrative Region in the northern Philippines.
The coast guard said more than 1,000 cargo truck drivers, workers, and passengers of over 20 vessels and cargo ships were stranded in over 30 ports in the affected regions.
At least 121 vessels and motorboats "are taking shelters" and prevented from venturing into rough seas, it added.
The state weather bureau warned that the typhoon will dump more rain in many provinces and regions, including in the capital Manila.
Molave, the 17th typhoon to batter the Philippines this year amid the Covid-19 pandemic, is currently blowing westward at 25 km per hour.
It is forecast to blow towards the South China Sea on Tuesday morning.
Typhoon Saudel, which battered the Philippines last week, also triggered flooding and displaced over 20,000 people.
It also damaged crops and roads, the agency said.
About 20 typhoons and tropical storms hit the Philippines each year.
The Southeast Asian archipelago of 110 million people has frequent earthquakes and volcanic eruptions.