While announcing the suspension of the services, the MTR said that passengers would not not be charged for their journeys, reports the South China Morning Post.
"We apologise for the disruption of your journey," it added.
Early Monday morning, about 20 protesters, many wearing masks, shut down the Cross-Harbour Tunnel in Hung Hom, a key link between Hong Kong Island and Kowloon, for the third straight day.
Within minutes, police with helmets and shields rush in and the protesters flee, with the roads quickly cleared.
Cries of "liberate Hong Kong, the revolution of our times" could be heard at several stations across the city.
Traffic was blocked on Lung Cheung Road, Wong Tai Sin, by barricades. But motorists removed them so they can drive through. No protesters, or police, were be seen at the scene.
Meanwhile, Hong Kong's Airport Authority has said that 209 flights have been cancelled at Hong as of 8.15 a.m., on Monday. Ten flights have already been cancelled for Tuesday.
Monday's development follows two days of intense stand-offs between protesters and police officers across the city from Western, Wan Chai and Causeway Bay to Kowloon and Tseung Kwan O, the South China Morning Post reported.
Clashes on Saturday night also resulted in tear gas fired and arrests.
The demands of protesters remain largely the same, including the full withdrawal of the now-suspended extradition bill and an inquiry into police actions over the handling of demonstrations.
( With inputs from IANS )