Abdul Wahid Siddibapa, a resident of Bhatkal in Karnataka, was held after his arrival from Dubai.
The NIA had started investigating the case following orders from the HC and the Ministry of Home Affairs.
Statement of Ashiq Ahmed — a 19-year-old engineering student from Bengal — along with those of two others, will form part of NIA chargesheet
NIA probe suggests main suspect was indoctrinated months in advance
The twin blasts occurred in the congested Bhikku Chowk on September 29, 2008, on the night of Shab-E-Qadr as residents were out shopping for Eid.
In the second supplementary chargesheet, the NIA dropped charges against Sadhvi Pragya Thakur and five other accused.
Avinash Rasal told The Indian Express after this newspaper reported on Friday that the NIA was likely to file a chargesheet watering down the case, he was bombarded with calls.
The NIA chargesheet submitted on Friday, which drops all charges against six of 11 accused, is at sharp variance with what the Maharashtra ATS and the earlier NIA had alleged in its chargesheet.
The Congress said the government had also questioned the integrity of people like public prosecutor Rohini Salian.
Minister of State for Home Kiren Rijiju rejected the charges saying it does not interfere in the investigation by the agencies while the BJP said Pragya was “framed” by the UPA government.
The bomb blast in Malegaon town near Nashik on September 29, 2008 had killed four and injured 79. The case was first investigated by the Maharashtra Anti-Terrorism Squad led by Hemant Karkare.
Kumar said the trial in most cases were moving at a good pace and he was confident that these would reach their “logical conclusion”.
Delhi Police had accused Shah of planning to carry out terror strikes in the national capital to avenge the hanging of Afzal Guru.
Ten years after a series of bombs exploded in Malegaon killing 37 people, the court had on Monday dropped charges against eight Muslim youths due to lack of evidence against them.
Eight of the accused, including Lt Col Purohit and Sadhvi Pragya, are in jail under MCOCA charges. They have also challenged application of MCOCA in the case.