"We resolutely support the action to maintain Hong Kong’s rule of law by the people who love the nation and the city, and we are determined to protect national sovereignty, security, stability and the prosperity of Hong Kong", the commander said as quoted by the South China Morning Post newspaper.
Protests on Saturday and Sunday witnessed violent clashes between the Hong Kong police and thousands of protesters.
The military commander warned that clashes would not be tolerated as they threatened the safety of Hong Kong citizens and went against the very essence of the "one country, two systems" model.
This is the first time when the Chinese military garrison chief has spoken on the civil unrest that erupted in Hong Kong in early June. Tens of thousands took part in the latest of a series of marches against a controversial bill that would allow extraditions to mainland China, despite Hong Kong leader Carry Lam saying the bill was dead.
In its turn, Beijing warned "external forces" of meddling in Hong Kong's affairs after the United Kingdom and the United States expressed concern over violence during protests.