In a statement, officials said operations had been "seriously disrupted" by the public assembly.
Many of those protesting are critical of the actions of police, who on Sunday were caught on film firing tear gas and non-lethal ammunition at close range.
Some protesters are wearing bandages over their eyes in response to images of a woman bleeding heavily from her eye on Sunday, having reportedly been shot by a police projectile.
In a statement on Monday, Hong Kong's Airport Authority said they were cancelling all flights that were not yet checked in. More than 100 flights scheduled after 18:00 local time (10:00 GMT) will now not depart.
I’d rather live with a good question than a bad answer.