The NIA, which had taken Arshi Qureshi into custody on November 30 along with two others, moved the court yesterday seeking its permission.
However, Qureshi did not give his consent to the procedure.
"The court has rejected the NIA application's after Qureshi did not consent to it and as per the Supreme Court guidelines, no tests can be conducted without the permission of the accused," said his lawyer Ishrat Khan.
He along with Rizwan Khan and Mohammed Haneef were booked based on a complaint made by Abdul Majid Abdul Kader - the father of Ashfaq, one of the 22 youths who had allegedly joined ISIS.
Mumbai-based IRF was banned by Union government last month for a period of five years under the Unlawful Activities Prevention Act.