The bus services were suspended in Mehsana, Patan, Gandhinagar, Sabarkantha and Banaskantha districts till the situation improves, he said.
There are two separate routes for north Gujarat - one from Gandhinagar to Himmatnagar in Sabarkantha, and another passes from Mehsana and stretches till Banaskantha district via Patan.
According to GSRTC secretary K D Desai, all the buses plying between Ahmedabad and the northern region have been cancelled since last night amid the fear of miscreants making these vehicles as their soft target.
Desai said though they tried to resume the service in Gandhinagar this morning, some people targeted a bus at a village in the district.
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"Thus, we have decided to halt the operations. We are in constant touch with police and will resume the service as soon as the situation becomes normal," he added.
Following the GSRTC's decision, several passengers were stranded at the state transport depots in the city, as they learnt about the cancellation of routes for north Gujarat upon their arrival here.
Last night, the agitators belonging to Rajput community allegedly set ablaze three buses in different parts of Mehsana. They also damaged the window panes of at least six buses in the region, the district's police control room said.
This morning, the agitators tried to block roads at Unava village near Gandhinagar and at Ambaji town in Banskantha, police said.
The Supreme Court had on Thursday paved the way for the nationwide release of "Padmaavat" on January 25 by lifting the ban on the screening of the controversial film in Gujarat and Rajasthan.
The top court passed the interim order on the petition by Viacom 18 Media Pvt Ltd and other producers of the movie, challenging bar on screening of the Sanjay Leela Bhansali- directed movie by Gujarat, Rajasthan, Haryana and Madhya Pradesh.