The five suspects, one female and four males aged between 20 and 22, were detained on August 14 and 15 after removing the Chinese national flag from a flagpole and throwing it into the sea on August 3-5, Xinhua News Agency cited the Hong Kong Police as saying.
The suspects' computers, phones and clothes have been seized by the police for further investigation.
According to the law, violators can face up to three years in jail for desecrating the national flag and coat of arms.
Mass protests erupted in China's semi-autonomous Hong Kong in early June in response to a controversial bill that would allow extraditions to the mainland. Although the local parliament eventually announced that it had suspended the bill, people continue to protest, demanding that it be withdrawn completely.
Several countries have already expressed concerns and advised their citizens against traveling to Hong Kong amid the escalation of public unrest.
China has repeatedly warned foreign nations against meddling in the affairs of Hong Kong.
On Wednesday, Xu Luying, spokeswoman for China's State Council's Hong Kong and Macau Office said that Beijing strongly condemned violent actions against two Chinese citizens, carried out by protesters at Hong Kong airport and called them "near-terrorist acts".
Xu emphasized that in the past few days "radical elements" in Hong Kong had completely crossed the line of law, morality and humanity.