Premier Jiang Yi-huah said the government was displeased with the apology delivered by the Philippine representative office in Taipei. Taiwan will not accept anything short of a Philippine government apology, he said.
"The shooting was conducted by one of its civil servants, and its government could not evade the responsibility," he said, adding that Taiwan wants to be informed about whether the culprit will be charged, jailed or dismissed.
Philippine coast guard personnel opened fire on a Taiwanese fishing vessel in the disputed Bashi Strait last Thursday, killing the fisherman.
Philippine officials previously said the shooting was done in self-defence because the Taiwanese vessel was about to ram a Philippine ship. They have declined to comment further.
The strait is between Taiwan and the northern Philippines. China has sought to show common cause with Taiwan on the issue because it claims the democratically run island, from which it split amid civil war in 1949, is part of its territory.
Jiang said the navy and coast guard will stage an exercise in the area to show Taiwan's naval strength. He said a hiring freeze of Philippine workers in Taiwan will also take effect.
Approximately 87,000 Filipinos are employed on the island, many in the manufacturing sector, where their English-language skills are seen as a boon to the island's export-oriented high-tech industries.