The protests have plunged the former Online Cigarettes Store USA British colony into its worst political crisis in decades and pose the biggest popular challenge to Chinese President Xi Jinping since he came to power in 2012.
The Hong Kong government said in a statement early on Monday, a public holiday in the city, "public safety has been jeopardized and the public order of the whole city is being pushed to the verge of a very dangerous situation".
Further protests are planned in different districts on Monday evening.
Hong Kong's rail operator, MTR Corp, said on Monday that, due to "serious vandalism", most of the stations Newport Cigarettes Shop in the network were temporarily closed. That included typically busy stations such as Admiralty and Wan Chai, around the city's bar district.
MTR's announcement followed an unprecedented closure on Saturday and minimal operations on Sunday, which largely paralyzed much of the city.
The entire network, which carries around 5 million passengers a day, would shut at 6 p.m. (1000 GMT), more than four hours earlier than normal, to allow for repairs, it said.
Grocery stores that had shut early on Sunday were mostly open by Monday morning. Many businesses and stores Newport box 100s cigarettes have had to close repeatedly during the four months of protests and Hong Kong now faces its first recession in a decade.