A Philippine minister said they were concrete blocks and a "prelude to construction", but photos taken recently at the disputed Scarborough Shoal show only natural rocks and coral jutting above the surface.
The photos, obtained by the South China Morning Post, appear to show rocks emerging at low tide at the same spot where Manila has claimed Chinese vessels were placing concrete structures.
The photos from the Philippines and Chinese sources could not be independently verified.
A fresh diplomatic quarrel between Manila and Beijing was triggered last week after the Philippine Department of Defence released air surveillance pictures showing a number of objects protruding from the water at Scarborough Shoal in the South China Sea, which China calls Huangyan Island.
The Philippines said the objects were concrete structures built by China, and warned that they could be a prelude to further construction, as China had done in 1995 on Mischief Reef, which the Philippines also claims.
Manila recalled its ambassador to China, Erlinda Basilio, to discuss how to handle the saga. Naval chief Vice-Admiral Jose Luis Alano said on Tuesday that Philippine officials were considering removing the structures.
Foreign Ministry spokesman Hong Lei said earlier that Manila's allegations were untrue and accused it of "creating trouble out of nothing".
The shoal, a series of rocky, low-lying islets about 220 kilometres off the main Philippine island of Luzon and 650 kilometres from Hainan province, has become the focus of a maritime stand-off between the two nations since last year.
Manila has accused China of taking control of the shoal by stationing vessels there and preventing Philippine fishermen from entering the area.
In January the Philippines asked a UN tribunal to rule on the validity of Chinese claims to the South China Sea. China has rejected the move, saying the dispute should be resolved through two-way talks.
US President Barack Obama will visit the Philippines, as well as Indonesia, Malaysia and Brunei on a Southeast Asian trip from October 6-12, the White House announced yesterday.