Talking to media after meeting EC officials, Naidu said, "The decisions of the Election Commission are very controversial, one-sided, pro-establishment."
Accusing the EC of supporting the government, Naidu said: "We are fighting against the Election Commission and it is very unfortunate for all of us".
He also questioned the EC for ordering re-polling in Andhra Pradesh after 25 days.
The TDP chief said action should be taken against BJP's Bhopal candidate Pragya Thakur for insulting Mahatma Gandhi.
"Even now you are not taking any action. If it is BJP MPs, Prime Minister, Amit Shah, you are not taking action. This is not right. I have complained to them (EC officials)," he said.
Thakur came under widespread criticism after describing Gandhi's killer Nathuram Godse as a "deshbakht" (patriot).
On West Bengal, Naidu said the Commission had no right to transfer any official. "It is against the spirit of federalism...transferring officials is akin to surrendering to the Central government," Naidu said.
He also targeted the EC for curtailing the election campaign in West Bengal by invoking Article 324 of the Constitution, raising questions over permission given to Prime Minister Narendra Modi to conduct two meetings in West Bengal.
"I am a senior politician of this country and I have seen so many elections. But I have never seen this type of (Election) Commission," he said.
With less than a week for announcement of Lok Sabha poll results, Naidu has planned meetings with several opposition leaders during his two day visit to the national capital.A
He met Communist Party of India-Marxist leader Sitaram Yechury and Aam Aadmi party leader and Delhi Chief Minister Arvind Kejriwal on Friday evening.
On Saturday, he is expected to meet Congress President Rahul Gandhi here and later Bahujan Samaj Party supremo Mayawati in Lucknow.