In a letter to Shah, the Commission referred to the purported remarks of West Bengal BJP leader Joy Banerjee made at a public meeting in Birbhum on September 20 that his party has "control over the Election Commission".
The poll panel also referred to his remarks on the security arrangements for the assembly polls in the state due next year.
"The Commission has directed that the Bharatiya Janata Party may explain its position with regard to the above statement of Banerjee. The reply of the party may be submitted by September 25," the EC said in a letter addressed to the BJP President.
Addressing a rally in Mayureshwar in Birbhum on Sunday, Banerjee had reportedly said his party has "control over the Election Commission" and it would ensure adequate deployment of central forces to oversee elections in West Bengal. He also said if BJP won the Bihar elections, it will "run a bulldozer" in Bengal in the next polls.
After the EC letter, BJP said it has nothing to do with Banerjee's remarks which he had made in personal capacity. It also noted that he has already apologised for his comments.
"The Election Commission is a constitutional body and BJP has all the respect for its independence," BJP secretary Shrikant Sharma said.