"He had questioned the independence of the Election Commission. It is a quasi-judicial body which delivers verdicts. Therefore, I have recused myself so that he can have faith in the independence of the institution," Rawat told PTI.
He said Kejriwal, the AAP and the people of the country should have full faith in the independence of the Commission.
"I thought it was the right thing to do," he said.
Another case relates to 27 AAP MLAs for allegedly holding office of profit.
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While the first case is at an advance stage of hearing, the second case is at its preliminary stage.
In an interview, Kejriwal had reportedly said he does not believe in the independence of two Commissioners, including Rawat because he comes from Madhya Pradesh and has been very close to Chief Minister Shivraj Singh Chauhan.
An IAS officer of the Madhya Pradesh cadre, he retired from service in December, 2014.