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The EC said his remarks at a press conference Sircilla on April 5 were violative of the provisions of the model code of conduct and its advisories.
The 48-hour ban of the Telangana former chief minister comes into force at 8 pm on Wednesday.
After Congress leader Randeep Singh Surjewala, Rao is the second politician to be banned from campaigning for 48 hours in the ongoing Lok Sabha elections.