Afzal Usmani is accused of involvement in the bombing campaign that saw 21 explosions within 70 minutes in the city of Ahmedabad, Gujarat state, which killed 56 people.
More than 200 people were injured in the low-intensity but deadly blasts, the Times of India reported.
All the bombs were planted in public places, including on parked bicycles, placed near bus stops and hidden inside hospitals.
Usmani escaped from custody as he and six other suspects were being transferred from Taloja Jail to the courthouse in south Mumbai.
In what the Hindustan Times said was "a glaring security lapse," Usmani escaped during lunch.
The case was adjourned to Monday when police are to file a report on the escape, The Hindustan Times report said.
Usmani was one of 21 Indian Mujahedin members arrested on charges of criminal conspiracy soon after the 2008 blasts in Ahmedabad and Surat.
The Ahmedabad attack July 26 came a day after seven smaller blasts killed two people in Bangalore. The following week, police found and defused about 20 bombs in Surat.
Usmani allegedly was involved in stealing four cars that were used to transport explosives to Ahmedabad and Surat, and also is charged with planting bombs, police said.
But since his capture in 2008, Usmani had been helping security agencies bust Indian Mujahedin cells in Mumbai.
The Indian government declared the Islamist militant group a terrorist organization in 2010 after it was blamed for an attack on a German bakery in Pune that killed 17 people.
The group also is blamed for three coordinated blasts in July 2011 in Mumbai that killed 27 people.
In September 2011, the U.S. State Department designated the Indian Mujahedin a foreign terrorist organization with significant links to Pakistan.
The State Department said the Indian Mujahedin maintains close ties to other U.S.-designated terrorist groups based in Pakistan including Lashkar-e-Toiba, Jaish-e-Mohammed and Harakat ul-Jihad-i-Islami.
"IM's stated goal is to carry out terrorist actions against non-Muslims in furtherance of its ultimate objective -- an Islamic caliphate across south Asia," the State Department report says.
"IM also played a facilitative role in the 2008 Mumbai attack carried out by LeT [Lashkar-e-Toiba] that killed 163 people, including six Americans."