Ambassador Erlinda Basilio flew back to Manila as the defence department this week accused China of laying 75 concrete blocks on disputed territory in the South China Sea, foreign department spokesman Raul Hernandez said.
"She was asked to come home for consultations, and she will (be in Manila) for the next few days," Hernandez told reporters.
He said Basilio was advising Filipino officials on how to handle the alleged Chinese actions at Scarborough Shoal, a rocky outcrop about 220 kilometres off the main Philippine island of Luzon, within the country's internationally recognised exclusive economic zone.
The outcrop is about 650 kilometres from Hainan island, the nearest major Chinese land mass.
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Asked if Manila would lodge a diplomatic protest or undertake other options, Hernandez said: "We are still studying the matter."
The Philippine foreign ministry earlier said President Benigno Aquino had also called off a planned trip to China on Tuesday for a trade fair after Chinese authorities imposed conditions on the trip.
The concrete blocks have raised concerns in Manila that China could be planning construction in the waters, as it did in Philippine-claimed Mischief Reef in another area of the sea, in 1995.
China claims most of the South China Sea, including waters close to the coasts of its neighbours.
Brunei, Malaysia, Taiwan and Vietnam also have competing claims to parts of the South China Sea, and the rivalries have been a source of tension for decades.
The Philippines engaged China in a tense standoff at Scarborough shoal in 2012.
Manila has said the Chinese had effectively taken control of the shoal by stationing vessels there and preventing Filipino fishermen from entering the area.
China has rejected the move, but has said it wants to solve the dispute through bilateral negotiations with concerned parties.