The Puri-Haridwar Utkal Express and Bhubaneswar-New Delhi Rajdhani Express are among th trains cancelled.
The South Central Railway has opened emergency control rooms and will maintain a liaison with the State Disaster Management Centre to update the possible effect of the cyclone in the section.
In a statement, the railways said 10 trains will be cancelled and another will be diverted on Thursday, Friday and Saturday.
There will be major changes in the pattern of traffic services due to the proposed dismantling of road-over-bridge in Kottayam yard (station limits) on Saturday.
The trains which were cancelled include the Amritsar-New Delhi Express, Amritsar-Chandigarh Express, Haridwar-Amritsar Janshatabdi Express and the New Delhi-Jalandhar City InterCity Express.
The Indian Railways said as many as 3 trains have been cancelled and 2 trains diverted due to the ongoing protest.
Following the protests, as many as four trains were diverted and 14 cancelled between Sawai Madhopur to Bayana section-Nimoda to Malarna block section in Kota Division of Western Central Railway.
A help desk was set up on the railway station premises to help the stranded passengers.
Passenger trains between Vijayawada and Visakhapatnam, Rajahmundry, Guntur and Bhimavaram were also cancelled.
The water level has touched the danger mark at a bridge between Ichhapuram and Jhadpudi stations in Berhampur-Palasa railway section, said Railways.
A Jansadharan Special will be run between Yesvantpur and Hassan.