Special judge Virender Kumar Goyal dismissed the bail plea noting that the investigation was at a crucial stage.
The agency has registered a corruption case against the 1988-batch IAS officer accusing him of trying to "settle" an ongoing probe being conducted by it against him.
The other accused -- Anand Agrawal, a relative of the officer, alleged middleman Bhagwan Singh and Syed Burhanuddin, who claimed to be an official of the Prime Minister's Office, are in judicial custody.
The CBI, however, had opposed the bail plea saying that a family member's medical condition cannot be considered for bail of the accused.
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"A person who is trying to influence the PMO and even trying to bend the course of investigation in his favour shows how influential he is," it had said.
The court had on March 21 dismissed the bail plea of Anand Agrawal in the case.
The agency has alleged that the officer had approached Bhagwan Singh, a Noida resident, who took him to Burhanuddin to get the graft case "settled".
The agency has registered a case of criminal conspiracy under the IPC and provisions of the Prevention of Corruption Act against the accused.
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