China claims nearly all of the disputed waterway, brushing off rival claims from other countries -- including the Philippines -- and an international arbitration tribunal ruling that its assertion has no legal basis.
It has deployed navy and coast guard vessels in recent months in a bid to bar the Philippines from strategically important reefs and islands in the South China Sea.
Three Chinese coast guard vessels and four smaller boats made "aggressive manoeuvres" towards two Philippine Bureau of Fisheries and Aquatic Resources ships and their inflatable boats on Friday near Thitu island, a Philippine Coast Guard statement said.
The Filipino vessels were transporting scientists intending to conduct a "marine scientific survey and sand sampling" at a sandbar off Thitu, the largest Philippine-occupied island in the disputed Spratlys chain, the coast guard said.
Thitu lies about 430 kilometres (267 miles) from the major Philippine island of Palawan and more than 900 kilometres from China's nearest major landmass, Hainan Island.
Chinese forces garrison the Subi Reef near Thitu.
Manila's coast guard said a Chinese navy helicopter "hovered at an unsafe altitude" above the Philippine fisheries agency's inflatable boats on Friday, "creating hazardous conditions due to the propeller wash".
"As a result of this continuous harassment and the disregard for safety exhibited by the Chinese maritime forces", the Philippine Coast Guard said it and the fisheries agency "regrettably suspended their survey operations and were unable to collect sand samples" from unoccupied sandbars off Thitu.
Despite the "dangerous confrontations", no accidents occurred, the Philippine coast guard said.
The Chinese coast guard said in a statement later on Saturday the Philippine boats had entered waters near Tiexian Reef, the Chinese name for Sandy Cay, a few kilometres from Thitu, and were forced to leave.
Those on board the Philippine boats "attempted to land illegally" to collect sand samples despite China's "unquestionable sovereignty".
"Chinese Coast Guard vessels intercepted, monitored, warned and repelled the Philippine vessels," the Chinese statement said.
Also on Friday, the same day as the incident near Thitu, Philippine forces resupplied and rotated without incident troops manning a derelict navy vessel grounded on the Second Thomas Shoal in the Spratlys, the foreign affairs department said.
Manila had deliberately grounded the vessel on the reef to assert its claim over the area.
The Philippine government raised the alarm this month over Chinese coast guard ships patrolling closer to the main Filipino island of Luzon, calling it an "intimidation tactic" by Beijing to discourage Filipino fishing.
China rejected the allegation, with a foreign ministry spokesman saying the patrols were "in accordance with the law".
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