The party announced that all scheduled programmes of Modi for the day have been cancelled except for one rally. Modi is expected to address a public meeting in Rohaniya assembly constituency.
The district administration had initially denied permission for all programmes, including a rally at Beniabagh. In a decision late Wednesday, it allowed Modi to hold some of the programmes.
But BJP general secretary Amit Shah said the approval came too late and they had no time to prepare for meetings. Hence, the party had decided to cancel the events.
Modi will arrive at the Babatpur airport in Varanasi by noon Thursday and will be taken to the Rohaniya rally venue in a chopper. He will then drive through the city to go to the party office where he will meet party workers.
Earlier, Modi had tweeted that he was sad as he was not allowed to take part in the Ganga Aarti at Assi Ghat.
The Gujarat chief minister also appealed Bharatiya Janata Party workers to remain calm and maintain discipline.
Senior BJP leaders led by Arun Jaitley, Ananth Kumar, state president Laxmikant Bajpai and Amit Shah will stage a sit-in outside the Banaras Hindu University gate, protesting against the poll panel.