Vice Admiral Jose Luis Alano said no further activity had been detected at Scarborough Shoal since the defence department accused China last week of laying 75 concrete blocks on an underwater section of the outcrop. The territory is claimed by both Manila and Beijing.
Discussions were under way about how to "address" the issue but the final decision on whether or not to remove the blocks rests with the Philippine government not the military, he said.
Filipino officials have warned that the block-laying could be a prelude to China building structures on the shoal, which lies just 220 kilometres off the main Philippine island of Luzon.
A Chinese foreign ministry spokesman last week denied that Beijing had laid concrete blocks on the outcrop, while asserting it was part of China's territory.
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The shoal is about 650 kilometres from Hainan island, the nearest major Chinese land mass, but China claims most of the South China Sea including waters near the coasts of its neighbours.
The Philippines engaged China in a tense standoff at Scarborough Shoal in 2012.
Manila has said the Chinese had effectively taken control of it by stationing vessels there and preventing Filipino fishermen from entering the area.
In January the government asked a United Nations tribunal to rule on the validity of the Chinese claims to most of the sea.
China has rejected the move, saying it wants to solve the dispute through bilateral negotiations with concerned parties.