"Airport operations at Hong Kong International Airport have been seriously disrupted, all flights have been cancelled", the administration said in a statement.
All passengers have been advised to leave the terminal buildings "as soon as possible" and contact their respective airlines to change flight arrangements.
The airport's online schedule showed the last flights complete the boarding. The Sky News website said the arrival flights that were already heading to the airport would be allowed to land.
Photos published by local media showed thousands of mostly black-clad protesters thronging the halls, holding up placards that read "Please Do Not Come to Hong Kong."
Local police earlier used tear gas and rubber bullets to disperse rallies in the city after protesters started throwing Molotov cocktails, injuring some officers.
Protests began more than two months ago after a local legislature opened debates on a bill that would have allowed extradition to mainland China. After mass rallies, city's chief executive, Carrie Lam has declared that the bill was "dead", but the unrest in the city continued.
As a result, over 500 protesters have been arrested, and almost 150 police officers have been injured over the past several weeks, according to Hong Kong Police Senior Superintendent Kong Wing-Cheung.