The United States has criticized China's build-up of military facilities on the artificial islands and is concerned they could be used to restrict free movement through the key trade route.
Philippine Defense Secretary Delfin Lorenzana's comment followed a December 30 broadcast of aerial footage by the official China Central Television showing Fiery Cross Reef, which appeared to have been transformed into an air base.
"The Chinese government said some time ago that they were not going to militarize those reclaimed islands," Lorenzana said, adding the protest would be made through the foreign ministry.
"If it is true and we can prove that they have been putting soldiers and even weapons systems, that will be a violation of what they said."
China has assured the Philippines it will not occupy new features or territory in the South China Sea.