The Commission has been under attack from political parties for not curtailing campaigning in nine Lok Sabha seats in the state from Thursday morning.
Opposition leaders also questioned the duration of ban on campaigning claiming that it has been done to favour the BJP in its campaign in the State.
The EC invoked Article 324 of the Constitution to curtail the campaigning for the last phase of the election on May 19.
BJP parliamentary party secretary Balasubrahmanyam Kamarsu said the delegation also apprised Naidu of the "murderous" attack on Shah.
The EC's action came a day after parts of Kolkata witnessed wide-spread violence during BJP president Amit Shah's massive road show in Kolkata.
Shah showed photographs as proof that TMC workers indulged in stone-pelting and arson aimed at him even while the CRPF personnel sought to protect him.
All eyes will be now on the Election Commission of India to ensure free and fair Lok Sabha polls in the state in the last phase on May 19, he said in a series of tweets.
A scuffle broke outside the Calcutta University campus on College Street, when student activists of both the Left and the TMCP shouted slogans against Shah.
BJP workers and people thronged the street to greet Shah, who is contesting the Lok Sabha election for the first time.