Two vessels were unhindered earlier on Tuesday in reaching the Sierra Madre, a ship intentionally grounded decades ago at the Second Thomas Shoal, Defense Secretary Delfin Lorenzana said in a statement.
A small boat was dispatched from a Chinese coast guard vessel with three people, who recorded the unloading of Philippine personnel and cargo, he said.
“I have communicated to the Chinese ambassador that we consider these acts as a form of intimidation and harassment,” Lorenzana said.
The Chinese Embassy in Manila did not immediately respond to Reuters’ request for comment.
A small contingent of military have for years been based on the rusty ship at the shoal to assert the Philippines’ claim to sovereignty in the area.
President Rodrigo Duterte on Monday told a summit hosted by Chinese President Xi Jinping that he “abhors” what took place at the shoal last week and that the rule of law was the only way out of “colossal” rows in the South China Sea.
China claims the majority of the South China Sea as its own, using a “nine-dash line” on maps that an arbitration tribunal in 2016 ruled had no basis under international law.
It has for years deployed hundreds of vessels in big clusters to reinforce its claim.
Brunei, Malaysia, the Philippines, Taiwan and Vietnam have competing claims.