Police were seen entering the airport building, and the cancellation of flights may be a preparation for a police clearance operation and the use of tear gas.
The Airport Authority said in a statement about 8pm Hong Kong time that it expected flights to resume at 6am on Tuesday and was working with airlines to reschedule flights.
A Virgin Australia spokeswoman said two flights, one from Sydney and the other from Melbourne, had landed or were soon to land in Hong Kong.
“Hong Kong International Airport will be processing inbound immigration for them,” she said.
Public transport from the airport was reportedly disrupted.
The Virgin Australia spokeswoman said it was important for the airline to assist their passengers arriving amid the police operation.
“We are working with authorities at the airport… we have ground crew at the airport,” she said.
Hong Kong media said other airlines had told ground crew to leave the airport early.
By 7pm Hong Kong time many protesters had left the airport, some by walking along the road to a nearby town.
Airport Express train services to Hong Kong continued to operate for arriving passengers.
A Qantas spokeswoman said four flights scheduled to depart Hong Kong for Australia on Monday evening had been impacted.
“We are contacting customers directly and will be providing updates once we have more information,” she said.
“We also had three flights that landed in Hong Kong this evening. Customers are being assisted by our team at the airport.”
A peaceful sit-in at the airport by demonstrators over the weekend had not disrupted passenger movements. But thousands more protesters wearing black continued to arrive at the airport on Monday afternoon, chanting loudly.
The protesters were calling out “black police return the eye”, angered that a female first aid volunteer was shot by police in the eye during street protests on Sunday evening.
Doctors said she was likely to lose her sight, prompting an angry reaction from 11 university student unions on Monday. Thousands of people dressed in black boarded trains to head to the airport.
The announcement that the airport would cancel flights came as Beijing’s top office on Hong Kong affairs gave an abrupt press conference, saying the protests “have begun to show signs of terrorism”.
“I am calling out here that Hong Kong has reached a critical juncture. All those who care about the future of Hong Kong should stand up firmly and say no to all criminal acts and say no to all violent elements,” said Yang Guang, spokesman for Hong Kong and Macau Affairs Office of the State Council.
“Stopping violence and restoring order are currently the most important and urgent task of Hong Kong that override anything else,” he said.
He read the statement in front of a handful of reporters, then left before answering any questions.
Hong Kong police in a press conference on Monday afternoon confirmed that officers had dressed as black-clad protesters on Sunday before arresting protesters in a clearance operation.
A police spokesman said a “small number of people conducted extreme violence” and an intelligence operation had led to the arrest of 15 “core members” of this group.
Arrested protesters were reportedly being held in an immigration detention centre near the Chinese border, with long delays to access lawyers.
Chinese state media released a video of the People’s Armed Police in armoured vehicles preparing for a drill in neighbouring Shenzhen across the border in mainland China.
On Sunday riot police had fired tear gas and rubber bullets inside two subway stations in dramatic scenes.
By the night’s end, 45 people had been hospitalised, the youngest aged eight.
Police had stormed the Tai Koo MTR station, rushing down the escalators, beating protesters with batons. Tear gas was fired at close range at a crowd of protesters at the top of the escalator.
Police commissioner Stephen Lo visited the hospital bed of a police officer he said had suffered burns when a protester threw a petrol bomb at Tsim Sha Tsui.
Police said in the press conference on Monday that protesters had paralysed roads on Sunday and encircled police stations.
Kirsty Needham is China Correspondent for The Sydney Morning Herald and The Age.