A bench of Justices R K Agrawal and A M Sapre said, "the writ petition is dismissed".
The apex court had on November 24 reserved the order in the matter.
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The Centre had opposed the plea, saying Asthana had an outstanding career and had supervised over 40 high-profile cases like coal scam, AugustaWestland scam, black money and money laundering cases.
Common Cause, the petitioner NGO, had opposed Asthana's appointment, saying it was illegal as his name had surfaced in a diary recovered during a raid conducted by the Income Tax department at the offices and other premises of company Sterling Biotech Ltd.
The Centre, however, had claimed that Asthana, who was earlier an additional director in CBI, was looking after its eleven zones.