Philippine President Rodrigo Duterte has ordered the navy to put up "structures" to assert sovereignty over a stretch of water east of the country where Manila has reported a Chinese survey ship was casing the area last year.
The Philippines has lodged a diplomatic protest with Beijing after the vessel was tracked moving back and forth over Benham Rise, a vast area east of the country declared by the United Nations in 2012 as part of the Philippines' continental shelf.
According to the Philippines, Benham Rise is rich in biodiversity and fish stocks.
China's Foreign Ministry on Friday said the ship was engaged in "normal freedom of navigation and right of innocent passage," and nothing more.
Defense Secretary Delfin Lorenzana said Duterte's instruction was to increase naval patrols in that area and put up structures "that says this is ours." He did not specify what structures would be erected.
"We are concerned, they have no business going there," Lorenzana told reporters late on Sunday.
Though he accepts China's explanation, Lorenzana said it was clear that its vessel was not passing through the area because it stopped multiple times, for sustained periods.
Lorenzana last week said he was suspicious of China's activities near Benham Rise and suggested they might be part of surveys to test water depths for submarine routes to the Pacific.
The issue was due to be discussed further at a national security council meeting on Monday evening, he said.
The issue risks disturbing ties with China at a time of rare cordiality between the two countries under Duterte, who has chosen to tap Beijing for business rather than confront it over its maritime activities and intentions in disputed waters.
Rows with China have usually been about the South China Sea, west of the Philippines, a conduit for about $5 trillion of shipped goods annually. China lays claim to almost the entire South China Sea.
While Duterte has been sanguine about ties with China, Lorenzana is more wary and has noted that Beijing's fortification of manmade islands inside the Philippines' 200 nautical mile exclusive economic zone has not abated.