"The foreign ministry has filed a strong protest while summoning the Philippines deputy representative to Taipei," foreign ministry spokesman Michel Lu told reporters.
The 68-year-old skipper of the 16-ton Manchunyi, Chen An-lau, died when a group of men fired on his boat off Luzon on Sunday, Taiwans coast guard said.
Chens brother, who was wounded in the attack, was transported back to Taiwan by coast guards for treatment Monday. Two other sailors on board, both from China, escaped unscathed.
Television footage showed the boat riddled with dozens of bullet holes.
Lu quoted Taiwans representative in Manila as saying that the Philippines had admitted firing at the boat for alleged poaching in its waters.
Meanwhile, the Department of Foreign Affairs (DFA) declined to comment on reports regarding Taiwans protest.
"This is pursuant to the one-China policy. But we attend to consular needs of Filipinos in Taiwan or wherever they may be," DFA spokesman Gilberto Asuque said.
The DFAs Asia Pacific Affairs Division said the department does not normally receive reports on similar incidents.
The STAR tried but could not reach Manila Economic and Cultural Office head Tomas Alcantara to comment on Taiwans protest. Pia Lee-Brago, AFP