The navy said in a statement a Robinson R22 helicopter with two officers on board was forced to make an emergency landing near a market south of Manila, Reuters reported.
The pilots were rushed to nearby hospitals, but eventually died from their injuries, the navy added.
The navy has only one R22 aircraft, it said, adding that an investigation is underway to determine what caused the crash and their aircraft are regularly maintained and inspected to ensure airworthiness.
"Nevertheless, no stone will be left unturned as we endeavour to prevent this kind of accident from happening again," the navy said.
The Philippines' military has suffered accidents involving its aircraft in the past and a program to upgrade military assets is underway.
In January 2023, two military pilots were killed when their plane crashed during a training flight.
In 2021, a military aircraft carrying troops bound for counter-insurgency operations crashed, killing 53 people in the worst military air accident in nearly three decades.