The Chinese players stormed off the pitch in Mainz on Saturday after a group of six spectators displayed the flags during the first in a series of friendlies against German fourth-division clubs.
With the match televised live in China, the junior players only agreed to continue after the protesters from "Tibet-Initiative Germany" - four Tibetan refugees and two Germans - took down the offending banners. They ultimately lost 3-0 to TSV Schott Mainz.
"We are firmly opposed to any country or any individual offering support to separatist, anti-China and terrorist activities or activities defending Tibet independence, in any form or under any pretext," foreign ministry spokesman Lu Kang told a regular press briefing today.
China has ruled Tibet since the 1950s, and has been accused of trying to eradicate its Buddhist-based culture through political and religious repression.
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Beijing insists that Tibetans enjoy extensive freedoms and that it has brought economic growth to the region.
Its officially atheist ruling Communist party views the Tibetan spiritual leader the Dalai Lama as a dangerous "separatist" campaigning for independence. He says he seeks only greater autonomy.
"We want to draw attention to the unlawful and violent occupation of Tibet and the suppression of fundamental human rights," one of the flag-bearing Mainz activists told the German Press Agency.
The Chinese juniors will play teams in Germany's fourth- tier Regionalliga Suedwest (south-west regional league).
Three teams have refused to face the Chinese after their fans protested, but the other 16 clubs in the 19-strong league will each be paid 15,000 euros (USD 17,634) for playing the junior team.
"We cannot ban the protests, there is the right to freedom of expression here and certain rules apply," said Ronny Zimmermann, vice-president of the German Football Association which has organised the matches.