The country's defense department on Sunday told China to follow international maritime laws "if it wants to earn the respect of the international community."
Defense Secretary Delfin Lorenzana made the remark after Liberian-flagged commercial vessel "Green Aura," manned by a Filipino crew, was reportedly harassed by Chinese Coast Guard vessels near Scarborough Shoal or Bajo de Masinloc on September 30.
At the same, Lorenzana said the issue "should not be blown out of proportion" since the ship was able to safely reach its port of destination "unimpeded."
"We, however, would like to reiterate our call for all countries to exercise prudence and respect freedom of navigation and passage" in the West Philippine Sea, he said.
"Bajo de Masinloc is well within the Philippine EEZ (exclusive economic zone), and the 2016 arbitral ruling declared that it is a common fishing area," he said.
An official report of the incident has been forwarded to the National Task Force on the West Philippine Sea for appropriate action, according to Lorenzana.
China claims most of the contested sea, including waters close to Philippine shores, and has rejected a UN-backed international tribunal ruling that invalidated its sweeping claims in the disputed waters.