Special CBI judge Santosh Snehi Mann denied bail to Prasad saying it was not a fit stage to grant him relief.
The agency had opposed the application saying that the accused was an influential person and if released on bail, he may tamper with the ongoing probe and flee from justice.
In his bail application, Manoj Prasad had said he was not required for the custodial interrogation and no purpose will be served by keeping him in further custody.
Manoj Prasad, arrested on October 17, is currently in judicial custody.
The court had on October 31 granted bail to co-accused and CBI's DSP Devender Kumar after the agency did not oppose his bail petition.
The Central Bureau of Investigation (CBI) had registered an FIR against Rakesh Asthana and others on a written complaint of businessman Sathish Sana on October 15.
Besides Rakesh Asthana, Manoj Prasad and Devender Kumar, another alleged middleman Somesh Prasad has also been named as an accused in the case The FIR had alleged that Devender Kumar, being the Investigating Officer (IO) in the case against meat exporter Moin Qureshi, was repeatedly calling the complainant to the CBI office to harass him and compel him to pay a bribe of Rs five crore for getting a clean chit in the case.
The complaint had also alleged that a part of the bribe was paid by Sathish Sana.