Defense Secretary Delphine Lorenzana said in a statement that the two ships had no obstacle to reach the Sierra Madre on Tuesday, after one ship was deliberately downed at the other Thomas Shoal decades ago.
He said a small boat was dispatched from a Chinese Coast Guard vessel with three people who recorded the unloading of Philippine personnel and cargo.
“I have informed the Chinese ambassador that we regard these acts as intimidation and harassment,” Lorenzana said.
The Chinese embassy in Manila did not immediately respond to a Reuters request for comment.
A small contingent of the military has been based on a rusted ship on the shoal for years to assert the Philippines’ claim to sovereignty in the area.
President Rodrigo Duterte told a summit hosted by Chinese President Xi Jinping on Monday that he “disgusted” what happened in the shoal last week and that the only way out of “huge” lines in the South China Sea was the rule of law .
China claims much of the South China Sea as its own, using the “nine-dash line” on the map that an arbitration tribunal in 2016 had no grounds for under international law.
It has deployed hundreds of ships in large groups over the years to bolster its claim.
Brunei, Malaysia, the Philippines, Taiwan and Vietnam have competing claims.