"Terminal operations at Hong Kong International Airport have been seriously disrupted as a result of the public assembly at the airport today," the airport announced in a statement sent to reporters.
All check-in service for departure flights has been suspended since 4:30 p.m. (4:30 a.m. ET), the airport authority added. Other departure and arrival flights for the rest of the day would continue, it said.
"Members of the public are advised not to come to the airport," it added.
Before the closure, flights had been taking off as the airport worked through a backlog even after a few thousand protesters once again occupied the arrival hall.
The closure came after the former British colony's embattled leader defied protesters calls to quit as the stock market tumbled and anti-government protesters filled the airport.
Unrest has roiled the Chinese semi-autonomous region for 10 weeks this summer, as thousands of residents chafe at a perceived erosion of freedoms and autonomy under Beijing's rule.
The increasingly violent demonstrations plunged the Asian financial hub into its most serious crisis in decades, presenting Chinese leader Xi Jinping with one of his biggest challenges since he came to power in 2012.
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For a fifth day, protesters occupied the arrivals hall at the airport, shut down in an unprecedented move on Monday that forced hundreds of flight cancellations. Beijing likened the demonstrations in Hong Kong to terrorism.
"Take a minute to look at our city, our home," Chief Executive Carrie Lam told a news conference at the government headquarters complex, fortified with 6-foot high water-filled barricades.
"Can we bear to push it into the abyss and see it smashed to pieces?" she added, her voice wavering.
As she spoke, the benchmark Hang Seng index hit a seven-month low. By lunchtime, it had dropped nearly 2 percent, dragging down markets across Asia. It has fallen 6 percent since the protests began in June.
The protests began as opposition to a now-suspended bill that would have allowed extradition to mainland China for those facing criminal charges, but have swelled into wider calls for democracy.
Demonstrators say they are fighting the erosion of the "one country, two systems" arrangement enshrining some autonomy for Hong Kong when China took it back from Britain in 1997.
They want Lam to resign. She said she would stay.
"My responsibility goes beyond this particular range of protest," she said, adding that violence had pushed the territory into a state of "panic and chaos."
"I, as the chief executive, will be responsible to rebuild the Hong Kong economy, to engage as widely as possible, listen as attentively as possible to my people's grievances and try to help Hong Kong to move on."
She did not respond to repeated requests to clarify if she had the power to withdraw the extradition bill to satisfy a key demand by protesters, or if she required Beijing's approval.
On Monday China said the protests had reached a critical juncture, after a weekend of street clashes in which both police and protesters appeared to toughen their resolve.
Police fired tear gas at the black-shirted crowds in districts on Hong Kong island, Kowloon and the New Territories.
A senior Chinese official said "sprouts of terrorism" were emerging in Hong Kong, given instances of violent attacks against police officers.
Hong Kong legal experts say Beijing might be paving the way to use anti-terror laws to restrain the protesters.
CORRECTION (Aug. 13, 2019, 7:37 a.m. ET): A previous version of this article misstated the extent of flight cancellations Tuesday at Hong Kong airport. All departing flights were canceled; arriving flights were disrupted but not canceled.