The resource-rich Spratly Islands are claimed in whole or in part by both nations, as well as by Brunei, Malaysia, Taiwan and Vietnam. Beijing has been creating artificial islands in the South China Sea, expanding former reefs and outcrops into guarded permanent outposts, increasing tensions with Washington, which has sent warships through the area.

Mr. Lorenzana said that Beijing had invoked an agreement between the Chinese and Philippine foreign ministers to maintain the status quo in the area, and not to occupy any new land features, in an effort to reduce tensions in the area. He said that Mr. Duterte had been informed of the “standoff” and had decided to halt construction on the sandbar.

“I agree with the decision because it was indeed a new feature,” Mr. Lorenzana said.

China claims ownership of a vast majority of the South China Sea, asserting rights even to waters near the shores of other nations.

A third of global maritime traffic passes through the South China Sea, making the disputes a source of contention, with defense strategists and analysts warning that competing ownership claims could lead to armed conflict.

The Philippines has contested many of China’s claims, but since assuming office last year, Mr. Duterte has taken a more conciliatory stance. The president, who is the current chairman of the Association of Southeast Asian Nations, hopes to begin negotiations this year for a code of conduct that would govern actions in the region. Mr. Duterte will host Asean leaders in Manila next week.