His comments came after the Philippine Coast Guard said Chinese navy vessels were detected last week during a government resupply mission to Filipino fishermen near China-controlled Scarborough Shoal.
The triangular chain of reefs and rocks lies 240 kilometres (150 miles) west of the Philippines' main island of Luzon and nearly 900 kilometres from the nearest major Chinese land mass of Hainan.
China seized the shoal from the Philippines in 2012 and has since deployed coast guard and other vessels that Manila says harass Philippine ships and prevent its fishermen from accessing a fish-rich lagoon there.
"It's worrisome," Marcos told reporters before departing for Australia where he will attend an ASEAN summit.
"Previously, only the China Coast Guard was operating in our area. Now their navy has joined in, along with fishing boats. So the situation is changing."
In the latest incident, a vessel belonging to the Philippine Bureau of Fisheries and Aquatic Resources received a radio challenge from a Chinese warship on February 21 as it sailed towards the shoal, the Philippine Coast Guard said on Sunday.
Another Chinese navy ship was detected 18.5 kilometres from the BRP Datu Sanday as it distributed fuel to Filipino fishermen near the reef on February 23, the coast guard said.
The Philippine Coast Guard also accused Chinese coastguard and other vessels of attempting to block the Datu Sanday near Scarborough Shoal on February 22.
Marcos insisted Manila would continue to "defend our maritime territory" and said Filipino fishermen should be allowed to fish in the country's waters.
China claims almost the entire South China Sea and has ignored an international tribunal ruling that its assertions have no legal basis.
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