CBI had sought 14 days' custody. Amin, a suspended Deputy Superintendent of Police, was arrested by the agency on Thursday from a hospital here.
The order on CBI's remand application had been reserved by Additional Chief Judicial Magistrate H S Khutwad yesterday after Amin alleged torture. "I was severely beaten up and also verbally abused by the CBI officers in custody," he had said.
The court today asked the agency to take him for a medical check-up and see to it that his health was protected.
CBI maintained in the remand application that before the alleged encounter of Ishrat Jahan and three others, no cordon had been set up, contrary to police's claim. "The incident did not happen in the way it was mentioned in the complaint," it said.
"The details of a widespread conspiracy to kill the deceased persons and the role played by each conspirator are yet not fully known. The accused person (Amin) knows these details and he has to be interrogated."
Police had then claimed that all four were terrorists who were on a mission to kill Chief Minister Narendra Modi.
As per Gujarat police's version, Amin was a part of the team which had cordoned off the area near the encounter spot and also took part in shoot-out.
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