Chinese Foreign Ministry spokesman Lu Kang said Beijing had lodged “stern representations” with the United States.
“The Taiwan issue is the most sensitive in China-U.S. relations,” he told a daily news briefing in Beijing.
Taiwan’s Defense Ministry said the two U.S. ships had sailed north through the Taiwan Strait and that they had monitored the mission.
Taiwan President Tsai Ing-wen said there was no cause for alarm.
“Nothing abnormal happened during it, please everyone rest assured,” she wrote on her Facebook page.
U.S. warships have sailed through the Taiwan Strait at least once a month since the start of this year. The United States restarted such missions on a regular basis last July.
The United States has no formal ties with Taiwan but is bound by law to help provide the island with the means to defend itself and is its main source of arms.
The Pentagon says Washington has sold Taipei more than $15 billion in weaponry since 2010.
China has been ramping up pressure to assert its sovereignty over the island, which it considers part of “one China” and sacred Chinese territory, to be brought under Beijing’s control by force if needed.
Beijing said a recent Taiwan Strait passage by a French warship, first reported by Reuters, was illegal.
China has repeatedly sent military aircraft and ships to circle Taiwan on exercises in the past few years and worked to isolate it internationally, whittling down its few remaining diplomatic allies.
The U.S. Defense Intelligence Agency released a report earlier this year describing Taiwan as the “primary driver” for China’s military modernization, which it said had made major advances in recent years.
On Sunday, the Preble sailed near the disputed Scarborough Shoal claimed by China in the South China Sea, angering Beijing.
CHINDIA ALERT: You'll be living in their world, very soon 