The Chinese Embassy in Manila, the Philippine capital, could not be reached for comment on Wednesday, which was a holiday in the Philippines commemorating its independence from Spain.

President Rodrigo Duterte of the Philippines has courted China as a strategic partner since he was elected in 2016. He was most recently in China last month, his fourth visit in three years, but bilateral ties have been fraying, particularly over territorial disputes.

The Philippine vessel, FB Gimber1, was anchored near Recto Bank in the South China Sea, a strategically important area that is claimed in whole or in part by China, the Philippines, Brunei, Malaysia, Taiwan and Vietnam. Manila calls the area the West Philippine Sea, and an international tribunal in The Hague ruled in 2016 that it was in the country’s exclusive economic zone.

China has refused to abide by the ruling, and Mr. Duterte has said there is no way to enforce it in the face of China’s military strength.

At a meeting of Asia-Pacific defense officials in Singapore this month, Mr. Lorenzana called on all South China Sea claimants to exercise utmost caution to prevent an escalation of hostilities. He pushed for freedom of navigation in the area, while the United States said it was investing heavily in new technology that would improve its defense capabilities along with those of its allies. Patrick Shanahan, the acting United States secretary of defense, also urged Beijing to follow a “rules-based order” in the region.