China claims most of the strategic and resources-rich sea and has controlled Scarborough Shoal, just 230 kilometres (145 miles) off the main Philippine island of Luzon, since a 2012 standoff with the Philippine Navy.
The Kalayaan Atin Ito (Freedom This is Ours) group said 16 of its members arrived near the shoal early yesterday, Philippine independence day, and their boat was promptly blocked by two Chinese coastguard vessels.
"They chased us with their two speed boats and blocked our path, sprayed water on us. Two of the swimmers however were able to reach the ring of the shoal and raised the Philippine flag."
The incident comes at a particularly tense time in the long-running dispute between the Philippines and China over Scarborough Shoal and other parts of the sea claimed by both.
China insists it has sovereign rights to nearly all of the sea, even waters close to the shores of its neighbours. Aside from the Philippines, other claimants are Vietnam, Malaysia, Brunei and Taiwan.
A ruling is widely expected over the next few weeks, although China does not recognise the arbitration and has reacted angrily to the Philippines' legal efforts.
Kalayaan Atin Ito has organised trips to Philippine-claimed or -controlled South China Sea islands in the past, sending 47 Filipino youths by boat to Filipino-garrisoned Thitu Island in the Spratly group in December.
The Philippine government has previously said it recognises the group's patriotism but has discouraged such trips, owing to safety concerns.
One clip showed a group of young men and women singing the Philippine national anthem while they stood on the deck of a wooden-hulled boat flying Philippine and United Nations flags.
A larger, white-hulled vessel is seen shadowing the Filipino vessel from behind.
Ban-eg said 15 Filipino youths and an American national took part in the protest sail, but did not identify the foreigner beyond calling the person a "volunteer".
A Chinese embassy spokeswoman in Manila told AFP it may comment later.
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