Scarborough Shoal lies 240 kilometres (150 miles) west of the Philippines' main island of Luzon and nearly 900 kilometres from Hainan, the nearest major Chinese land mass.

China claims almost the entirety of the South China Sea despite a 2016 court ruling that said its claims had no basis in international law.

Beijing revealed plans in September to create a "nature reserve" at Scarborough, prompting Manila's former national security adviser Eduardo Ano to call it a "clear pretext towards eventual occupation".

Foreign affairs department spokeswoman Analyn Ratonel confirmed on Tuesday that Manila had issued a protest over the new structure, said to be located at the entrance of a lagoon once used by Filipino fishermen.

Manila "has undertaken the appropriate diplomatic action, such as several demarches and the issuance of a formal protest, against the structure", Ratonel told reporters in a messaging app group chat.

The message came a day after Philippine military chief of staff Romeo Brawner told a government television station that air force planes had spotted a structure with six people atop it and what appeared to be an antenna.

"We will not allow a repeat of what happened in the past when they initially put up a small structure and then later on it grew into an artificial island," he said in an apparent reference to reefs in the area that China has turned into militarised islands.

"We will not allow that at Scarborough Shoal," he said, pledging increased air and sea patrols to monitor developments in the area.

In a statement, the Chinese embassy in Manila repeated Beijing's "indisputable" claim to Scarborough as part of its "inherent territory".

"It is fully within China's sovereign rights to carry out activities including scientific research at Huangyan Dao," embassy spokesman Ji Lingpeng said, using China's name for Scarborough Shoal.