"We quash the press note issued on August 19, 2008," a bench of justices Dipak Misra and U U Lalit said.
Nisha Priya Bhatia, a former RAW officer, had moved the court seeking various reliefs including a direction to the Centre to "forth with" take back the press note as it is "defamatory" and "false".
Earlier, the court had asked the Centre to file its reply within three weeks.
The former intelligence officer had recently been in controversy for filing a PIL against the Chief Justice of India H L Dattu. The plea was dismissed by the High Court.
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Bhatia was compulsorily retired from service for security reasons after her identity became public in 2009.
She was in news for her alleged attempt to commit suicide before the PMO after alleging sexual harassment by her senior officers in 2008 and due to the disclosure of her identity as a RAW officer.