The incident happened Saturday as the Philippine Coast Guard escorted charter boats carrying food, water, fuel and other supplies to Filipino military personnel stationed at Second Thomas Shoal in the Spratly Islands.
Beijing claims almost all of the South China Sea, through which trillions of dollars in trade passes annually, and has ignored a 2016 international court ruling that its assertion has no legal basis.
The Philippine military and coast guard have accused the China Coast Guard of breaking international law by blocking and firing water cannon at the resupply mission, preventing one of the charter boats from reaching the shoal.
Another charter boat successfully unloaded its cargo.
"Our Secretary of Foreign Affairs summoned Ambassador Huang (Xilian) today and gave him a note verbale including pictures, video about what happened, and we are awaiting their reply," Marcos told reporters.
"The position of China, of course, is they say 'this is ours so we are defending it', and we, for our part, are saying 'no, we own it so we are defending it'. So that becomes a grey area that we are discussing."
China maintained over the weekend that it had taken "necessary controls" against Philippine boats that "illegally" entered its waters.
The US State Department on Sunday condemned the Chinese actions, saying they directly threatened regional peace and stability.
Britain, Australia, Canada and the European Union also criticised Beijing's conduct.
Second Thomas Shoal is about 200 kilometres (124 miles) from the Philippine island of Palawan, and more than 1,000 kilometres from China's nearest major landmass, Hainan island.
China's coast guard and navy vessels routinely block or shadow Philippine ships patrolling the contested waters, Manila says.
The Philippines has issued more than 400 diplomatic protests to Beijing since 2020 over its "illegal activities" in the South China Sea, the foreign ministry said.
China appeared to be "trying to gauge our commitment to supply our troops" at the shoal, National Security Council spokesman Jonathan Malaya told reporters on Monday.
"For the record, we will never abandon Ayungin Shoal," Malaya added, using the Philippine name for Second Thomas Shoal, located in the Spratly Islands.
- 'David and Goliath' -
Malaya said Saturday's "David and Goliath" incident showed the Chinese had established what appeared to be a "blockade" of the shoal.
"There were only two (Philippine) coast guard vessels and two Philippine supply boats against six large Chinese coast guard vessels and two Chinese militia vessels, and more People's Liberation Army naval vessels at near proximity to the area," he said.
Malaya said he believed it was the largest Chinese presence at the shoal "in recent memory".
At one point, a China Coast Guard vessel came "within 20 yards (18 metres)" of a Philippine coast guard boat, which he said could have resulted in a collision.
The National Task Force for the West Philippine Sea, which includes representatives of various government agencies, condemned the Chinese actions "in the strongest terms".
"As a low tide elevation, Ayungin shoal can neither be the subject of a sovereignty claim nor is it capable of appropriation under international law," the task force said in a statement.
Second Thomas Shoal was part of the Philippines' exclusive economic zone, and the resupply and upkeep of the BRP Sierra Madre were "legitimate Philippine government activities", it added.
The Philippine military deliberately grounded the Sierra Madre on Second Thomas Shoal in the late 1990s, and keeps up a tiny garrison there to maintain a presence in the hotly contested waters.
In a statement on Monday, the Chinese coast guard urged Manila to "tow away" the ship and "restore the reef to its original state".
Manila and Beijing have a long history of maritime disputes over the South China Sea, but former Philippine president Rodrigo Duterte was seen as cozying up to China in the hope of attracting investment.
Since succeeding him, however, Marcos has insisted he will not let China trample on his country's maritime rights, seeking to strengthen defence ties with former colonial ruler and longtime ally the United States.
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