A coast guard report said the boat Tawash was on its way to Guimaras province with 36 passengers and five crew members when it overturned.
The squall or violent gust of wind was not believed to be connected to Typhoon Koppu, which struck northeastern provinces of the Philippines on Sunday.
Coast guard rescuers and passing vessels recovered 32 survivors. Among the dead were two boys aged 6 and 9 and two of the crew members.
A 3-year-old boy is among the missing. The report said due to strong current and big waves, rescuers failed to retrieve the boat.
Koppu blew ashore into northeastern Aurora province with fierce wind and heavy rains early yesterday, leaving at least two dead, forcing more than 16,000 villagers from their homes.