Lodhi (31) was arrested by the premier investigating agency from Gurdakheri village in Hatod tehsil of Indore district yesterday.
The court of Chief Judicial Magistrate Priyadarshan Sharma granted three-day transit remand to NIA which has to produce Lodhi in a Maharashtra Control of Organised Crimes Act (MCOCA) court in Mumbai on Monday, said Lodhi's counsel Ranjan Sharma.
Earlier, the defence pleaded that Lodhi be granted a one-day custody.
35 people were killed as four bombs planted in the communally-sensitive powerloom town of Malegaon had exploded on September 8, 2006.
Malegaon had seen another terror attack in 2008.