Beijing is Berlin's top trade partner but Germany published a new policy in July to contend with a more "assertive" China after months of wrangling within the government over its strategy.
Baerbock, who has pushed for a more hawkish line, made the remarks in a Fox News interview on September 14 during a visit to the United States.
While talking about the Ukraine war, she said: "If Putin were to win this war, what sign would that be for other dictators in the world, like Xi, like the Chinese president? So therefore Ukraine has to win this war."
China said on Monday it was "strongly dissatisfied" and that it had made "solemn representations to the German side through diplomatic channels".
"(The comments) are extremely absurd and are a serious infringement of China's political dignity and an open political provocation," foreign ministry spokeswoman Mao Ning said at a daily news conference.
Berlin's new China policy marks a fine balance between the two differing positions in its coalition government, calling Beijing a "partner, competitor, systemic rival".
Baerbock, of the German Greens, has pushed for a harder line against China and for a greater emphasis on human rights, while Chancellor Olaf Scholz, a Social Democrat, has backed a more trade-friendly stance.
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