Bhatkal and Akhtar were produced in the court on Thursday after they were interrogated by the Bihar Police and the NIA, reports said.
The NIA will bring Bhatkal to Delhi on Friday.
Bhatkal was arrested from Bihar on Wednesday night.
Earlier in the day, Union Home Minister Sushilkumar Shinde confirmed the arrest of Bhatkal.
"He (Yasin Bhatkal) has been arrested from Bihar along India-Nepal border last night," said Shinde, confirming the news of 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.
"This is a major catch and it would degrade IM," said former Indian Home Secretary RK Singh.
Opposition Bharatiya Janata Party (BJP) leader Jaswant Singh said now the administration should build on the arrest.
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.
After the arrest of Bhatkal, his father Zarar Siddibapa and uncle Yaqub Siddibapa in a statement to media said "he should be punished if he is guilty of any offence after the due process of law is followed." They said the family is relieved after his arrest.
They said the family has full faith in judiciary and there should not be any media trial.
The statement said Yasin was born in the village of Bhatkal in 1983 and after failing in tenth grade in 2005 he had left for Dubai. His father said he disappeared from Dubai in 2007.
"The truth will come out and our fears that he would be eliminated in a fake encounter have been put to rest," they said, adding that the arrest put to rest their fear that he would be killed in a fake encounter.
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 29-08-2013)