The protest came after Chinese warships passed through Sibutu Strait in the southern Philippines without authorization and some 113 Chinese vessels were detected last week around Pag-asa island - known as Thitu island internationally - one of the largest of the disputed Spratly archipelago.
National Security Adviser Hermogenes Esperon said at a press conference on Wednesday that he had recommended the filing of the protest over these two incidents in a verbal note to Foreign Affairs Secretary Teodoro Locsin, Efe news reported.
"Diplomatic protest fired off," Locsin tweeted soon after.
Speaking on the matter of Sibutu, Esperon said that all the military vessels that pass through Philippines territory seek diplomatic authorization, but there was no record of China seeking a diplomatic clearance for those vessels.
Philippines' Defence Secretary Delfin Lorenzana - who had accused China of bullying in the disputed waters - initially informed last week that Chinese warships were passing through Sibutu Strait and that it had happened four times since February.
Esperon said that according to China, it was an innocent passage through the usual maritime route and it was right in that sense, but according to their agreements and practices with other countries, diplomatic clearance was advisable, according to the report.
Esperon said there was currently one Chinese coast guard vessel and one fishing boat in the region.
He added that the government erected five lighthouses and would build five more to protect the territory and waters of the Philippines while the country would also acquire an unmanned high-flying aircraft for satellite imagery.
In April, Philippines filed a diplomatic protest due to the presence of some 200 Chinese vessels around the Pag-asa island - some unofficial reports indicated more than 500 of them - which forced China to withdraw more than a hundred such vessels.
According to the Philippines Navy, by the end of May, there were only 18 Chinese vessels, but throughout July their presence increased and Beijing militarized the South China Sea by employing paramilitary forces in maritime disputes vis-à-vis other claimants, a Pentagon report said.
In 2016, the Permanent Court of Arbitration at the Hague recognized Philippines' rights to some territories in the South China Sea region, including Scarborough Shoal and part of the Spratly archipelago, where China has constructed de facto military bases on the man-made islands.
( With inputs from IANS )