In unusually blunt remarks on a local Hong Kong matter, Zhang Xiaoming, Beijing's top representative in the semi-autonomous city, told reporters the violence that left dozens of police officers hurt also showed elements of "terror".
"After the riot in Mong Kok, we are feeling very much shocked and saddened," Zhang told reporters.
"We strongly condemn those radical separatists who have become increasingly violent, even (carrying out) activities that showed terror tendencies," the director of China's Liaison Office in Hong Kong said in Chinese.
Police fired warning shots in the air, while demonstrators hurled bricks levered up from pavements, charged police lines with homemade shields and set rubbish on fire.
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About 100 people were injured, including police officers, journalists and protesters, and 65 were arrested in the disorder, rare in Hong Kong.
Some 30 of them have been charged with rioting.
Hong Kong leader Leung Chun-ying said today most of the protesters were unemployed and did not reflect mainstream views.
The battles have been dubbed the "fishball revolution" after a favourite Hong Kong street snack and reflect underlying tensions over the erosion of the city's traditions.
Demonstrators included "localist" activists who want to restrict Beijing's influence on the city.
Mong Kok, on the city's Kowloon peninsula, was the scene of some of the worst violence during the 79-day "Occupy" pro-democracy street protests in late 2014.
The mass rallies seeking fully free leadership elections in the city blocked some major streets for more than two months.
But there are fears that freedoms enshrined in the agreement are being eroded by Chinese influence, including the recent case of five Hong Kong publishers known for titles critical of Beijing, four of whom it is confirmed have been detained on the mainland.