In a letter to BJP leader Arun Jaitley, the EC said the protests were announced despite the poll body trying to resolve the matter "in accordance with law and the ground situation".
Principal Secretary in the EC R K Srivastava said while earlier a BJP representative Vidyasagar Rai had requested for an alternative site on May 6, Jaitley later urged the returning officer not to process the permission.
"In the whole matter, the Commission decided not to go by the version conveyed by the district magistrate alone, but consulted the UP Chief Secretary and the DGP, who endorsed the security and suitability aspects including capacity of the ground (in Veeniya Bagh), raised by the district officials.
The letter said the Commission has given prompt attention to any issue raised by political parties, including BJP, over the ongoing elections.
"Hence the Commission is surprised and disappointed that your party has chosen to hold protests over the matter, which was being sought to be resolved in accordance with law and ground realities," it said.