The airport suspended check-ins for departing flights - its second straight day of major service disruptions - as embattled local leader Carrie Lam warned that the city risked sliding into an "abyss".
The chaotic situation eventually ended when protesters allowed ambulance workers to take the man away on a stretcher.
Protesters said they detained him because he wore a press vest and claimed to be a reporter, but a mainland Chinese ID card was found in his belongings.
The group apologised for clashes on Wednesday, in which police armed with batons and pepper spray clashed with thousands of protesters, saying that "after months of prolonged resistance, we are frightened, angry and exhausted".
After mass flight cancellations on Monday and Tuesday, Hong Kong's airport resumed operations, although many remain delayed or cancelled.
"We express the strongest condemnation of these terrorist-like actions", said Xu Luying, spokeswoman at the Hong Kong and Macao Affairs of the State Council, who called the two men " mainland China compatriots".
The Royal Thai Consulate-General suggested that Thais due to board flights at the airport on Tuesday and today should consult their airlines for updates on the status of their flights and avoid protest-ridden areas at the airport if at all possible.
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At the heart of the demonstrations is Hong Kong's proposed legislation which dictates that certain suspected criminals be deported to mainland China where they could face more harsh treatment, including torture and unfair trials.
It comes as Hong Kong enters its tenth week of anti-government protests.
Beijing is sending increasingly ominous signals that the unrest must end, with state-run media showing videos of security forces gathering across the border.
Britain, a guarantor of the agreement that transferred Hong Kong to China in 1997, on Tuesday condemned the violence and urged dialogue. "Everyone should be calm and safe!" he commented.
Demonstrators who have been protesting for the past nine weeks against Beijing's growing influence in the special administrative region targeted the global airport for a second day on Tuesday. They have been seen on a number of occasions hurling bricks and other items at riot police, while a police officer over the weekend was injured by a "petrol bomb".
"I very much hope that even after 10 weeks of this going on, the government and President Xi will see the sense in establishing a way of actually bringing people together". The actions of the protesters "seriously damage the worldwide image of Hong Kong, and seriously hurt the feelings of a vast number of mainland China compatriots", said Xu, saying the "extremely abominable violent crime must be severely punished according to the law".