By mid-morning, commuters were crammed into stations across the city, waiting to board trains that were badly delayed, with no service on some lines.
Rail operator MTR Corp urged people to seek other transport.
Transport Secretary Frank Chan called on protesters to stop targeting a rail network that provides transport to five million people a day, public broadcaster RTHK reported.
Hong Kong, which returned to China in 1997, is embroiled in its worst political crisis for decades after two months of increasingly violent protests that have posed one of the gravest populist challenges to Communist Party rulers in Beijing.
China on Monday reiterated its support for Hong Kong’s embattled leader, Carrie Lam, and its police and urged Hong Kong people to oppose violence.
Lam’s popularity has dropped to a record low, according to a survey by the independent Public Opinion Research Institute released on Tuesday.
The survey, conducted between July 17 and July 19, showed Lam scored a rating of 30.1, down from 33.4 at the beginning of the month. Her approval rate stands at 21%, while her disapproval rate is 70%.
Over the last few years, many people in Hong Kong have become concerned about the whittling away of the city’s freedoms, guaranteed under a “one country, two systems” formula established when it returned to China in 1997.