Sea travel in the Philippines can be hazardous. Traveling by ferry is not recommended due to safety concerns. Ferries are often overloaded, lack necessary lifesaving equipment and are not adequately maintained.
Pump boats are often used for short trips between islands but this type of travel is only suitable for those prepared to rough it out. Remember that storms can develop quickly and can be very dangerous.
In addition to these safety issues, there is a high incidence of piracy and armed robbery against ships in and around Philippine waters. If you choose to utilize this mode of transportation prepare accordingly by checking travel forums and websites for updated information on companies with reliable reputations.