Manila accused a Chinese security vessel of "aggressive actions", saying it used a military-grade laser light against a Philippine patrol boat in the disputed waters -- over which China claims almost complete sovereignty.
The February 6 incident has escalated into a diplomatic row, with Marcos later summoning Beijing's ambassador in Manila to express "serious concern" over the rising frequency of maritime events.
On Saturday, he warned cadets at a military academy of "heightened geopolitical tensions that do not conform to our ideals of peace and threaten the security and stability of the country" as well as Asia and the rest of the world.
"This country will not lose one inch of its territory," he said in the northern city of Baguio without naming China.
"We will continue to uphold our territorial integrity and sovereignty in accordance with our constitution and with international law."
Beijing has defended its actions, saying the Philippine boat "intruded" into China's sovereign waters without permission and its Coast Guard responded in a "professional and restrained" manner.
But Manila insists the Philippine patrol boat crew were temporarily blinded by the laser.
Beijing has ignored an international court ruling that its claims over much of the sea have no legal basis.
The Philippines, Vietnam, Malaysia and Brunei all have overlapping claims to parts of the sea.
Days before the latest incident, US defence secretary Lloyd Austin was in Manila to shore up a deal that gives US troops access to another four military bases in the Southeast Asian country.
Washington and Manila also agreed to resume joint patrols in the South China Sea, with Austin saying his country's commitment to Philippine security was "ironclad".
He added that their mutual defence treaty extends to Philippine troops, public vessels or aircraft anywhere in the South China Sea.
On Saturday, Marcos told reporters he will not invoke the mutual defence pact with the United States over the laser incident because it could "provoke" tensions instead of cooling them down.
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