"Whether they are neutral or pretending to be so, only you know," he shot back at reporters when asked if he thought the Commission was neutral in its actions.
Karunanidhi, however, did not elaborate.
Meanwhile, state Chief Electoral Officer (CEO) Praveen Kumar refused to be drawn into the controversy saying he did not want to comment.
"I don't to comment on such things as a rule. Everyone has a right to express views," he said when reporters sought his response on the DMK chief's remark.
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Party's Rajya Sabha MP T K Rangarajan submitted a petition to the CEO pressing for the withdrawal of the order.
Kumar had earlier said district collectors have been asked to implement prohibitory orders under Section 144 of Cr.PC till 6 am of April 24, the polling day, to prevent last-minute money distribution and maintain law and order.
Such orders are clamped during 'extraordinary times' or when there are law and order situations, Rangarajan said adding implementation of the same during elections will 'hamper just election work.'