President Ma Ying-jeou reiterated that the Philippines should take formal responsibility for the death of the 65-year-old, shot last week by Philippine coastguards who said his vessel intruded into Philippine waters.
Amid outrage in the island, Taipei has slapped sanctions on Manila, including a ban on the hiring of new Philippine workers, a travel alert urging Taiwanese not to visit the Philippines and the suspension of high-level exchanges.
Manila said it had "gone the extra mile" to try to appease Taipei and expressed concern that a special envoy sent to the island had been rebuffed.
The ships went as close as 21 nautical miles west of Batan but stayed within Taiwan's exclusive economic zone, said Rear Admiral Lee Tung-pao.
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"The move is aimed to highlight our determination to safeguard sovereignty. The coastguards have vowed to protect our fishermen wherever they are, and we'll support them," Lee said.
The fleet did not encounter any Philippine naval or coastguard vessels.
Two Taiwanese Mirage 2000-5 fighters flew over the fleet at low altitude as the warships tested their anti-aircraft capabilities.
The Philippines expressed some indignation at Taiwan's treatment of its envoy Amadeo R. Perez, sent by President Benigno Aquino to apologise personally to the victim's family.
Perez left Taiwan earlier today after Foreign Minister David Lin and the fisherman's family refused to meet him.
"I came to convey the president's and the Filipino people's deep regret and apology over the unfortunate and unintended loss of life," he told reporters at the airport before his departure.