Philippine ships have been harassed several times in recent months by Chinese vessels in the disputed waterway, an important trade route where other Southeast Asian countries such as Malaysia, Vietnam and Indonesia also have claims.
Marcos told the 18-nation East Asia Summit, which was attended by China, that Manila was concerned about the installation of military facilities on reclaimed features such as outcrops and reefs, as well as violations of international law.
"We are concerned over consistent actions that are in violation of obligations under international law," Marcos said, according to a transcript of his remarks released by the presidential palace.
"We must oppose the dangerous use of coast guard and maritime militia vessels in the South China Sea."
He did not mention any country by name at the summit, which was attended by Chinese Premier Li Qiang and US Vice President Kamala Harris.
Chinese coast guard vessels fired water cannon on August 5 at a Filipino ship on a mission to resupply marines stationed at a World War II-era ship on Second Thomas Shoal.
Another resupply mission to the shoal was also harassed later that month. China defended its actions in the area as "professional".
The Philippines deliberately grounded the ship to stake its claims on the shoal in the disputed sea, which China claims almost in its entirety.
China, which has built military facilities on reclaimed territory, has urged the Philippines to remove the ship.
It has also used boats, which Manila described as "militia vessels", to enforce its claims against smaller neighbours.
Marcos said countries must not allow tensions in the South China Sea to escalate further and urged "all parties to exercise self-restraint and refrain from unilateral" actions that would increase tensions and risk miscalculations.
China released a new map ahead of Association of Southeast Asian Nations meetings in Jakarta this week in which its maritime claims overlapped with those of other countries.
The map sparked strong protests from Malaysia, the Philippines and Vietnam.
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