Citing a statement by the spokesman of China's Taiwan Affairs Office, Xinhua said officials in Kaohsiung should not "obstinately insist" on showing the film, which "distorts the facts and glorifies a separatist".
"Do not stir up trouble for cross-strait relations again," the Chinese statement said, although it did not spell out possible consequences of screening the film.
China has claimed sovereignty over self-ruled Taiwan since 1949, when Mao Zedong's forces won the Chinese civil war and Chiang Kai-shek's Nationalists fled to the island.
The two sides have tried to improve relations over the past year, but Kaohsiung, a stronghold of Taiwan's opposition Democratic Progressive party which supports Taiwanese independence from China, angered Beijing when, along with several other opposition-led counties, it invited the Dalai Lama to pray for victims of Typhoon Morakot, which killed up to 770 people last month.
Beijing sees the Tibetan leader and Kadeer as separatists.
Kadeer has strongly denied Chinese accusations that she was behind the ethnic violence in July in China's western Xinjiang region between Uighur and Han groups that left almost 200 people dead, according to the government.
A furore erupted in Australia earlier this year when the Chinese embassy pressed unsuccessfully for the same documentary to be removed from the country's biggest film festival in Melbourne, prompting an angry public backlash and higher audience numbers.