The MTR Corporation, the city's railway operator, also confirmed that cross-border train services resumed early Tuesday morning, reports the South China Morning Post.
For travellers heading to mainland China, both the Guangzhou-Shenzhen-Hong Kong Express Rail Link and cross-border intercity trains were offering normal services on Tuesday morning.
On Monday morning, 10 scheduled cross-border intercity train services were cancelled, including five departing and five arriving.
Congestion was also widely expected at the global transport hub, which handles an average of 200,000 travellers each day, after dozens of flights were rescheduled for Tuesday.
On Monday, Hong Kong's local airlines cancelled about 250 of 1,000 passenger flights after air traffic controllers, flight attendants, pilots and ground crew called in sick en masse in support of the anti-government strike.
The Cathay group, which also owns budget carrier HK Express, advised customers against going to the airport unless their flight had been confirmed and to arrive three or four hours early because of overburdened security checkpoints.
Twelve departing flights and 37 arrivals were however, cancelled on Tuesday.
On Monday, Carol Ng Man-yee, chairwoman of the pro-democracy Confederation of Trade Unions, estimated about 350,000 people went on strike, while 290,000 attended seven rallies around the city on Monday, the South China Morning Post reported.
Monday's strike was the latest in protests that have rocked the city for more than two months.
Protesters demand the full withdrawal of the now-suspended extradition bill, which has already been shelved, and an independent investigation into the government's handling of the political crisis.
( With inputs from IANS )