Hanoi said its vessels collided with Chinese ships near waters off the Paracel Islands, where a Chinese oil company is establishing a rig. And in the Spratly Islands, a Chinese fishing boat was apprehended by Philippine maritime police.
The three countries have had increasingly tense disputes over areas of the South China Sea. The Chinese foreign ministry rebuked both nations for disturbing the "normal operations" of vessels in Chinese waters.
Ministry spokesman Hua Chunying said the movements in the Paracel Islands were "within China's sovereignty and not related to Vietnam".
Hanoi said the drilling was illegal and sent patrol vessels to the area, resulting in at least three collisions with Chinese boats since Beijing said it was drilling on Saturday.
The deputy commander of Vietnam's maritime police, Ngo Ngoc Thu, said the Chinese "actively used water cannon to attack Vietnamese law enforcement vessels".
"Some Vietnamese people were injured by broken glass as a result of the clash," he said.
In the other flashpoint, Beijing sent a maritime police vessel to the Half Moon Shoal in the Spratly Islands, where the Chinese fishing boat was seized by Philippine maritime police, and made representation to Manila.
The vessel with 11 crew was seized on Tuesday along with 350 marine turtles. Charges of catching endangered green sea turtles would be laid, the Philippine government said, calling it a move to "uphold sovereign rights".
Hua hit back, saying: "We demand the Philippines give a reasonable explanation, and immediately release the vessel and the crew members on board."
Chinese fishermen said several armed men forced themselves onto two fishing vessels, one of which escaped.
"Up to 10 warning shots were fired," said a crew member.
Observers said the incidents indicated there would be more confrontations, though military clashes were unlikely. "The suspicions among these nations are widening," said Zhang Mingliang , an expert in regional affairs at Jinan University.
Du Jifeng, of the Chinese Academy of Social Sciences, said: "New conflicts will emerge when old ones are not resolved."
Additional reporting by Associated Press, Agence France-Presse, Reuters