The judge on Friday said Bhatkal and his close associate Asadullah Akhtar alias Haddi will remain in NIA custody for the next 12 days for interrogation.
A special plane was arranged to commute the "deadly" terrorist from Patna to Delhi.
Earlier on Thursday, a Bihar Court granted a three-day transit remand of Bhatkal and Akhtar to the NIA.
Bhatkal and Akhtar were produced in the court on Thursday after they were interrogated by the Bihar Police and the NIA, reports said.
Union Home Minister Sushilkumar Shinde on Thursday confirmed the arrest of one of India's most wanted terrorists, who has been on the run for five years and was actively involved in even planting the bombs himself as caught in CCTV camera footage.
Reports said some of his movements were tipped off by the US federal investigating agency FBI.
The 30-year-old Bhatkal's arrest is seen as a major success of the Indian agencies.
Hailing from Karnataka, his real name is Mohammed Ahmed Siddibappa and there was a Rs 10 lakh reward on him announced by the NIA, which investigates the terror attacks.
Indian Mujahideen (IM) has carried out several attacks against civilian targets in India. It is a front for the Pakistan based Lashkar-e-Taiba. Bhatkal co-founded IM in 2008 with his brother Riyaz Bhatkal and Abdul Subhan Qureshi.
IM is responsible for major strikes like the Pune's German bakery blast where CCTV footage also captured him planing the bomb. He was also reportedly seen at the scene of the Hyderabad blast in Feb this year. He had executed attacks in Bangalore and Ahmedabad too killing over 50 people in the blasts in the Gujarat city in 2008.
In May 2008 after bombings in Jaipur that killed over 60, IM had sent an e-mail to Indian media in which they claimed responsibility for the attacks.
Investigators believe that Indian Mujahideen is one of many groups composed of lower-tier SIMI members. SIMI or Students Islamic Movement of India is a banned Islamic student organisation that was formed in Aligarh, Uttar Pradesh, in 1977.
The Indian Mujahideen was branded a terrorist organisation by India in June 2010. Countries like USA and others also declared IM a terror outfit.
--IBNS (Posted on 30-08-2013)