“The German side’s behaviour increases security risks and sends incorrect signals,” Chinese military spokesperson Li Xi said in a statement.
Beijing’s troops in the area would “resolutely counter all threats and provocations”, Li added.
German defence minister Boris Pistorius confirmed on Friday that the frigate Baden-Wuerttemberg and the supply Frankfurt am Main sailed through the strait.
US military ships as well as those operated by other countries have often sailed through the sensitive waterway.
But the Baden-Wuerttemberg’s voyage was the first time in more than two decades that Berlin’s navy had done so, according to German media reports.
Beijing views Taiwan as a renegade province and claims jurisdiction over the body of water that separates the island from the Chinese mainland.
Germany and many other countries argue such voyages are usual, citing freedom of navigation.
China’s Li said Saturday that the People’s Liberation Army had sent sea and air forces to “monitor and warn off” the German vessels.