Bhatkal and his close aide Asadullah Akhtar were produced before the court in muffled faces amid tight security after expiry of their seven-day NIA custody.
The NIA wanted Akhtar to be remanded to judicial custody. Its Hyderabad unit moved a separate plea seeking permission to formally arrest Akhtar in connection with the February 21, 2013 blasts in Hyderabad's Dilsukhnagar area.
The Court allowed the Hyderabad NIA unit's plea and sent Akhtar to two days transit remand in connection with the case.
The twin blasts had claimed 16 lives and were triggered by IEDs planted near Konark and Venkatadiri theatres in Dilsukhnagar area of Hyderabad on February 21.
During the hearing, the NIA sought eight days custody of Bhatkal saying he had travelled to different parts of India in furtherance of the conspiracy to carry out terror strikes.
"The objective of the investigation of the case is primarily to uncover each and every aspect of the activity of IM and their hidden sleeper cells and operatives so that the number of terrorist activities being planned by the outfit could be prevented," the NIA said.
The NIA also told the Court that Bhatkal had associates in Pakistan, Nepal and Middle East who were also involved in the case and more information regarding them have to be ascertained during his custodial interrogation.
"I have perused the case diary and am satisfied that the accused Mohd Ahmed Siddibappa alias Yasin Bhatkal is required for interrogation. The accused Yasin Bhatkal is remanded to police custody for four days upto September 22," District Judge I S Mehta said.
NIA told the Court that it has to go through large number of emails having secret codes, secret email IDs and chat IDs and Bhatkal's custody was required to ascertain the facts regarding these.
Regarding Akhtar, the court directed NIA's Superintendent of Police of its Hyderabad unit, to produce him before the special NIA court there on or before September 19.
"I have perused the contents of application filed by SP NIA Hyderabad and the same is allowed. The permission for arresting accused Asadullah Akhtar is granted to CIO/SP NIA Hyderabad and two days transit remand is given to NIA Hyderabad," the Court said.
Meanwhile, advocate M S Khan, who appeared for Bhatkal, opposed the NIA plea, saying there were no specific allegations against his client and that the agency had not come out with any new facts to seek police custody.
Advocate Mehmood Pracha, who appeared for Akhtar, opposed the plea of NIA's Hyderabad unit saying the probe agency has already interrogated him for 19 days.
The special cell of Delhi police, ATS Maharashtra and Bangalore Crime Branch have also moved separate applications seeking custody of Bhatkal and Akhtar.
According to the NIA, Bhatkal, wanted in around 40 terror cases and carrying a reward of Rs 35 lakh, and Akhtar were arrested from the Indo-Nepal border on the night of August 28.
Bhatkal was among the "principal conspirators" and "executors" of various terror attacks in India, the NIA has said in its charge sheet filed in a Delhi Court last month.
Bhatkal, who hails from Bhatkal village of Udupi district in North Karnataka, is wanted in a string of terror attacks in Ahmedabad, Surat, Bangalore, Pune, Delhi and Hyderabad, the agency said.


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