Presidential Communications Undersecretary Claire Castro confirmed to reporters Marcos had summoned Chinese ambassador Jing Quan on Tuesday.
Earlier in the day, China's foreign ministry said it summoned Manila's envoy to China.
The summoning of ambassadors comes a day after the Philippines and China accused each other over an encounter in the Second Thomas Shoal of the South China Sea.
Philippine officials said one of its navy personnel was struck on the head but Beijing said Manila provoked the incident.
"The Philippine side provoked the incident first, yet has turned around and made counter-accusations, distorted the facts and engaged in malicious hype," the Chinese foreign ministry said.
The China Coast Guard (CCG) said on Monday two rubber boats sent by the Philippines' grounded vessel BRP Sierra Madre rammed into a Chinese patrol boat in the South China Sea and the Philippine personnel initiated "malicious attacks" against Chinese law enforcement officers by using oars and long sticks.
Such diplomatic summons are relatively rare despite frequent tensions between China and the Philippines in the South China Sea.
Tuesday's announcement marks the third publicly reported instance of China summoning the Philippine ambassador during President Ferdinand Marcos Jr's administration, following summonses in January 2024 after the Philippine president congratulated Taiwan leader-elect Lai Ching-te on his election victory, and in November 2024 over Manila's enactment of the Maritime Zones Act and the Archipelagic Sea Lanes Act.
China's foreign ministry has also, over the years, called in the Philippine ambassador to make representations - a less severe diplomatic step than a formal summons - over issues including disputes in the South China Sea and Taiwan-related matters.
Marcos was last publicly reported to have summoned the Chinese ambassador in 2023 after a Chinese coast guard ship directed a military-grade laser against a Philippine coast guard vessel.
China's foreign ministry called the actions taken by the Philippines during Monday's encounter "egregious in nature".
Manila accused Beijing of aggressively striking one of its navy personnel on the head with a wooden baton and said one navy rubber boat was damaged.
In a separate statement on Tuesday, the CCG said China permitted the Philippine side to transfer the injured personnel through small shuttle boats from the grounded Philippine warship "out of humanitarian consideration".
"The CCG inquired and verified the Philippine boats, and monitored the whole process," CCG spokesperson Jiang Lue said, adding China would continue to carry out "rights-protection and law-enforcement operations" in waters near the Second Thomas Shoal.
The Philippine military on Tuesday called China's claims "false and misleading", saying its personnel did not initiate any confrontation.
