Manila's defence minister on Tuesday accused the Chinese coastguard of "intimidation and harassment" after Philippine navy personnel were filmed and photographed unloading goods in the disputed South China Sea.

Tensions over the resource-rich waters have spiked in the past week after Chinese coastguard ships fired water cannon at Philippine boats delivering supplies to marines at Second Thomas Shoal in the contested Spratly Islands.

Manila expressed outrage over the attack which forced the Philippine boats to abort their mission. But Beijing said the vessels had entered its waters without permission.

China claims almost all of the waterway, through which trillions of dollars in trade passes annually, with competing claims from Brunei, Malaysia, the Philippines, Taiwan and Vietnam.

Beijing has ignored a 2016 ruling by The Hague-based Permanent Court of Arbitration that its historical claim is without basis.

Two civilian boats manned by Philippine Navy personnel made another attempt to reach the shoal and arrived "without any untoward incident" on Tuesday, Defence Secretary Delfin Lorenzana said.

But three people in a rubber boat deployed by a nearby Chinese coastguard vessel took photos and videos as "personnel and cargo" were unloaded from the vessels, Lorenzana said. 

"I have communicated to the Chinese ambassador that we consider these acts as a form of intimidation and harassment," he added.

The Chinese embassy in Manila did not immediately respond to a request for comment.

After China occupied Mischief Reef in the mid-1990s, the Philippines ran a derelict navy vessel aground on the nearby Second Thomas Shoal to assert Manila's territorial claim. Members of the Philippine marines are based there.

Tuesday's incident comes a day after Philippine President Rodrigo Duterte condemned the latest flare-up in the sea during an Asian regional summit hosted by Chinese President Xi Jinping.

"We abhor the recent event in the Ayungin Shoal and view with grave concern other similar developments," Duterte told the meeting, using the Philippines' name for the shoal.

"This does not speak well of the relations between our nations and our partnership." 

Duterte's remarks were unusually strong for a leader who has fostered warmer ties with Beijing since taking power in 2016 in the hope of extracting promised investment and trade.