Top BJP leaders Arun Jaitley, Amit Shah and Ananth Kumar sat on a dharna outside the Banaras Hindu University protesting against the refusal and the alleged partisan approach of the returning officer Pranjal Yadav.
In Delhi, workers sought to protest outside the Election Commission but the Delhi Police stopped them a short distance away while imposing prohibitory orders in the area.
The assault on Election Commission was led by Modi, a candidate in Varanasi, who was denied permission to address a meeting in Beniabagh, a communally sensitive area chosen by the BJP.
"It is unfortunate that EC is not concerned about the institution's neutrality. That is why our 'karyakartas' (workers) have to embark on a Satyagraha," he said on Twitter.
Jaitley, who has been campaigning in Varanasi for the last few days, also hit out at the Commission, saying he cannot conceal his disappointment with the Election Commission.
"Men in constitutional offices need to be bolder. Timid men can dwarf high offices," he said. Jaitley alleged that by condoning the Returning Officers stand on 'No-Modi rally' in Varanasi city the Commission has used the security card to prevent the BJP Prime Ministerial candidate's right to campaign in his constituency.
"If you can't ensure security, don't hold the polls in the country. But if you do hold the polls please provide a level playing field," the BJP leader, who is camping in Varanasi, said. He said the EC cannot deny the candidate the right to campaign.
"Rahul Gandhi can have a road show in Varanasi but Narendra Modi cannot have a rally. The security card is selectively used," he said.