Chief Metropolitan Magistrate Vinod Yadav asked Pune ATS to explain as to why Siddiqui, who had been arrested by the Delhi police for his alleged role in several terror cases, including Pune German bakery blast, was not produced before him after the expiry of his custody with them.
The court's order came on an application by Siddiqui's counsel M S Khan seeking to know as to why his client was not produced before the CMM by the Pune ATS despite lapse of four weeks since his custody was handed over to them on May 1.
The CMM had on May 1 handed over Siddiqui's custody to the Pune ATS for four weeks for interrogation in connection with the German Bakery blast.
When his case was taken up by the CMM on May 29 after expiry of four weeks since grant of his custody to Pune police, Siddiqui was not produced before him and on June 8, he was reportedly killed by fellow inmates in Pune Yerwada jail.
Khan also sought to know as to why Siddiqui was kept in Yerwada jail.
"I find substance in the application of the defence counsel. Let an explanation be called from ATS Mumbai, Maharashtra in this regard for the next date, July 3," the court ordered.
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Meanwhile, the communication received from ATS Mumbai along with the copy of FIR on Siddiqui's killing, the inquest proceedings and the medical notification of his death was also placed before the court.
Twenty six-year-old Siddiqui was found dead in his cell in high security Pune jail on June 8 morning.
A native of Bihar, he was apprehended by Special Cell of Delhi Police on November 22 last year.
Siddiqui was one of the 11 alleged IM operatives, arrested by the Special Cell and was named in almost all the cases ranging from Chinnaswami stadium blast to the Jama Masjid blast and firing incident and the Pune German bakery blast.