The Taiwanese frigates, armed with anti-ship missiles, made no contact with the Japanese vessels during their hour-long patrol near the uninhabited islands north of Taiwan.
Both Tokyo and Taipei claim that the islands, whose waters are rich in fish, fall within their exclusive economic zones.
Japan often fines ship owners and impounds Taiwanese fishing vessels that enter the waters, and the decision to send the frigates followed complaints by fishermen that Taiwan has not done enough to protect them.
Fifteen Taiwanese lawmakers escorted by Defense Minister Lee Jye left aboard one of the frigates as it departed Taiwan's eastern Suao port for the four-hour round trip. The legislators waved Taiwanese flags and chanted patriotic slogans but Lee did not appear on deck.
Japan's representative in Taipei, Tadashi Ikeda (search), said Monday that it was inappropriate for Taiwan to bring its military into a fishing dispute.
Some fishermen expressed doubts about how effective the government's action would be.
"We appreciate (the action)," said Tsai Shui-ho. "But if they only go out on patrol today and don't go out tomorrow, I don't think it will help to solve the problem."
But Taiwanese Premier Frank Hsieh said Japan might now be compelled to settle the fishing dispute through negotiations.
"There may be overlapping of our exclusive economic zones, but we can discuss it and don't have to chase away the other side's boats," he said.
Taiwan has long avoided sending warships to the waters, fearing conflict with its neighbor and major trading partner.
Although Taiwan and Japan do not have diplomatic ties, Taipei tries to maintain close relations with Tokyo, seeing it as an effective military counterweight to China, the island's biggest security threat.
China, which considers Taiwan part of its territory, urged Japan to respect the rights of Taiwanese fishermen in disputed waters.
China "expresses strong dissatisfaction" at Japan's actions and believes Tokyo should "properly and prudently address the issue," Foreign Ministry spokesman Liu Jianchao said Tuesday.