Special CBI Judge M B Gosavi while discharging Amin observed that there was no sufficient evidence against him.
The Maharashtra government had argued in the apex court that all pleas seeking an independent probe into Loya's death were motivated and aimed at targeting "one individual" in the guise of upholding the rule of law.
Raising security issues, the defence lawyers referred to a media report on the death of a judge who had dealt with the case and said "misreporting has already caused prejudice to both sides". They said it was a "sensational" case and some untoward incident could happen if publication of reports was allowed.
The Supreme Court on Friday termed as a "serious matter" the issue of alleged mysterious death of special Central Bureau of Investigation judge B H Loya, who was hearing the Sohrabuddin Sheikh encounter case, and sought response from the Maharashtra government on pleas seeking an independent probe into it.
The apex court also asked to see "all documents" in the Loya death case.