Delays affected the Mass Transit Railway (MTR) as scuffles broke out on Monday between commuters and activists, who held open the doors to stop trains leaving. Several MTR lines were also suspended.
Air traffic controllers called in "sick en masse", echoing the actions of an estimated 500,000 Hongkongers from more than 20 business sectors, the South China Morning Post reported.
The number of flights that could take off, or land, were affected as a result, and authorities said only one of the two runways would be in operation till 6 a.m. on Tuesday.
Flights around Asia bore the brunt of the cancellations, the report said.
Most of the cancelled flights were with local carriers Cathay Pacific and Hong Kong Airlines. Besides these airlines, Cathay Dragon and HK Express also advised passengers to check before they travelled to the airport on Monday.
One video circulating on Twitter reportedly showed a car in the district of Yuen Long forcefully hitting a barricade set up by protesters, injuring one person, according to the BBC.
The strike is part of the protests that have rocked the city for more than two months, with protesters demanding full withdrawal of a now-shelved extradition bill that would have allowed extradition to mainland China.
But these demonstrations have evolved into a catch-all movement against the local government and are causing disruptions. The protesters are now demanding an independent inquiry into the police violence, resignation of the territory's Chief Executive Carrie Lam and democratic reform.
There were violent clashes on Saturday and Sunday and the police again fired teargas at protesters on Monday.
Police officials said they fired 1,000 teargas canisters and 160 rubber bullets and had made 420 arrests since June 9, when the anti-government protests began.
In her first media address in two weeks, the city's leader Carrie Lam said the protesters' actions had challenged the principle of "one country, two systems" and were threatening prosperity and stability in Hong Kong.
She also accused activists of using the extradition bill as a "cover" for their "real goals".
"We continue to allow these violent protesters to make use of the (extradition) bill to conceal their ulterior motives. Those ulterior motives are going to destroy Hong Kong."
She said that she would be not be stepping down one of the demands made by protesters.
It was not yet clear how many joined the city-wide strike, but several shops and businesses were closed. Activists also scheduled rallies in seven different parts of Hong Kong on Monday.
( With inputs from IANS )