Neeraj Sharma, the spokesperson for Northern Railway, said that 485 trains were affected by the violence in Punjab and Haryana, out of which 445 were cancelled.
The Delhi Transport Corporation has also suspended its inter-state, night and the Delhi-Lahore bus services that pass through the two states.
Railway officials said mobs had attacked stations in Malaout and Balluanna during the day.
The Swarna Shatabdi and the Shan-e-Punjab shuttling between Amritsar and New Delhi have been cancelled.
Other trains going to the capital that are cancelled include the Jammu Rajdhani, Uttar Sampark Kranti Express and the Shri Shakti Express.
The Lucknow-Chandigarh Express was cancelled as well as the Pashchim Link Express which travels between Bandra Terminus in Mumbai, and Kalka in the Panchkula district, where 28 people were killed yesterday.
The Haryana Express, travelling from Tilak Bridge in New Delhi to Sirsa, where the headquarters of the Dera Sacha Sauda is located, has also been cancelled.
Other trains cancelled in Haryana include the Link Express from Haridwar to Una Himachal and the Unchahar Express which goes from Chandigarh to Prayag.
The Ambala Cantt-Kalka, Delhi (Old Delhi Junction)-Kalka, Ambala Cantt-Patiala and Firozpur Cantt-Ludhiana Junction passenger trains were also among the list of trains cancelled.
The violence erupted when a court in Haryana found Gurmeet Ram Rahim Singh guilty for the rape of two women in a case dating back nearly 17 years.
PM Narendra Modi has condemned the violence, saying he was "deeply distressed".
Sporadic incidents of violence were also reported from the national capital Delhi. Two buses and two empty train coaches were set on fire by mobs.
The instances of violence today are deeply distressing. I strongly condemn the violence & urge everyone to maintain peace.— Narendra Modi (@narendramodi) August 25, 2017