Bettina Stark-Watzinger signed the Science and Technology Agreement with Taiwan's National Science and Technology Council (NSTC) on the first day of a trip that drew sharp criticism from China.
Beijing views the self-ruled, democratic island as its territory, to be taken one day -- by force if necessary. China routinely opposes official exchanges between Taiwan and its international partners.
It has ratcheted up military, diplomatic and economic pressure in response to a flurry of visits by politicians from the United States, Europe and elsewhere to Taiwan.
At the signing ceremony in Taipei, Stark-Watzinger said it was "a great pleasure and honour" for her to be the first German government minister to visit in more than two decades.
"This arrangement stands for enhancing cooperation on the basis of democratic values, transparency, openness, reciprocity and scientific freedom," she said.
China's foreign ministry said the country "firmly opposes" the "malicious" visit.
"China has lodged solemn protests and expressed strong dissatisfaction with the German side in Beijing and Berlin," said spokesman Wang Wenbin at a regular press briefing on Tuesday.
He said China had urged Germany "to immediately stop its collusion and interaction with the separatist forces in Taiwan, to immediately stop sending them the wrong signal and to immediately stop using the Taiwan question to interfere in China's internal affairs".
Stark-Watzinger declined to comment when asked about Chinese opposition to the visit.
Germany's foreign ministry last week reaffirmed its commitment to a "one China" policy, wherein it has formal bilateral ties with Beijing, but also maintains "close and good ties with Taiwan".
Wu Tsung-tsong, head of the NSTC, said the trip was part of "normal" exchanges. It comes two months after a high-ranking German parliamentary delegation travelled to Taiwan.
The agreement covers joint research in several fields, Wu said, including semiconductors and artificial intelligence.
According to media reports, Taiwanese tech giant TSMC, the world's largest contract chipmaker, is currently in talks to build its first European plant in Germany.
In December, the company said that there was "no concrete plan" for setting up facilities in Germany.
burs-aw/aha/leg
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