Manila filed a political protest on Friday over ‘endless shipping, long stays, and illegal acts of Chinese marine vessels and fishing vessels’ in an area near the island of Titus.
It demanded that its great neighbor withdraw ships.
The Chinese embassy in Manila did not immediately respond to a request for comment other than working hours.
Tensions between Manila and Beijing have intensified over months of the presence of large Chinese ships in the Philippines' special economic zone. The Philippines says it believes the ships were controlled by the military, and Beijing said they were fishing boats protected from the elements.
"The islands of Pag-asa are an important part of the Philippines where they control themselves," the Foreign Ministry said in a statement.
Tito, known as Pag-asa in the Philippines, is 451 kilometers (280 miles) from the mainland and is the largest of the eight islands, shields, and islands found on the Spratly islands.
China has built a small town with airstrips, hangar and upstream arches on the S Subi Reef about 25 kilometers (15 miles) from Titus.
This is at least the 84th political protest the Philippines has filed against China since President Rodrigo Duterte took office in 2016.
The international court that year dismissed China's growing claim in the South China Sea, which exceeds $ 3 trillion in shipping. Brunei, Malaysia, the Philippines, Taiwan and Vietnam also have conflicting interests on various islands and features in the area.
Duterte concealed the favorable decision and made a reunion with Beijing with the aim of securing billions of dollars in loans, aid and investments, much of which awaited him.