Squads of riot police arrived shortly before midnight after thousands of demonstrators again flooded the terminal buildings during the day.
Flight departures were brought to a standstill amid scuffles.
At least three men were mobbed inside the airport by protesters.
They were said to be holding identity cards showing they were police officers from mainland China.
Hong Kong police have admitted deploying officers disguised as anti-government protesters during the unrest in the city.
But the editor of China's Global Times newspaper said one of those attacked was one of his reporters who was merely doing his job.
The airport, one of the world's busiest, has been the site of daily protests since Friday. It has become the latest focus of mass political unrest in Hong Kong that began 10 weeks ago and shows no signs of abating.
The wider anti-government protests started in June in response to a proposed extradition bill, which has now been suspended, but have evolved into a more demanding pro-democracy movement. They are being fuelled by fears that the freedoms Hong Kong enjoys as a special administrative region of China are being eroded.