Maritime Security is another important function of the PCG. Considering the archipelagic character of the country, it is vital to enhance the security of its different maritime zones to protect the integrity as a nation. In the performance of this function, the PCG contributes to maintain good order at sea by conducting regular patrols and surveillance for the safety of navigation of ships, to safeguard ships from illegal acts and to promote freedom of navigation.

The PCG is likewise mandated to secure exploration and resource utilization activities within the country's maritime jurisdiction.

In its Sea Marshal Program, the PCG manages composite security forces composed of AFP, PNP and PCG elements to protect voyages of passenger-laden vessels in domestic routes. The Coast Guard also boasts of a newly established nationwide K-9 unit composed of highly trained sniffing dogs deployed in the major ports throughout the country.