Sadhvi Pragya Singh Thakur along with Shamlal Sahu and Shivnarayan Singh, all hailing from Madhya Pradesh, were produced before a chief judicial magistrate K D Boche in Nashik in Maharashtra which remanded them to police custody till November 3.
Public prosecutor Ajay Miisar said the crime committed by the three was a "serious offence" and they were booked under charges of murder, attempt to murder and voluntarily causing grievous hurt under IPC Sections 302, 307 and 326 respectively.
The sadhvi, who is based in Indore but who regularly visited Surat to give lectures, was picked up from the diamond city by the Anti Terrorist Squad of the Mumbai police. Shamlal Sahu and Shivnarayan Singh were brought from Indore in MP for questioning to Mumbai. The arrests were made in the last one week.
Misar said the motorcycle used in the Malegaon blasts on September 29 in which five persons were killed belonged to the sadhvi. Besides having links with the Bharatiya Janata Party's student wing the Akhil Bhartiya Vidyarthi Parishad, she is suspected to be associated with the Indore-based radical Hindu Jagran Manch accused of involvement in the blasts in Malegaon as well as in Modasa in Gujarat in which one person was killed. The right-wing outfit has denied the charge.
Misar claimed that following the Malegaon blasts the sadhvi, who also is believed to be a member of Surat-based Vande Mataram Sanghatan, had several telephone conversations -- all lasting "400 minutes" -- with the other two.
Misar said forensic reports have shown that RDX was used in the Malegaon blasts.
The state had asked for 14 days custody, but the court gave only 11 days' custoday, he added.
Pragya's father Chanderpal Thakur said he does not believe his daughter was involved in the blasts.
"Her nature would not have allowed her to do something like this. It is a different thing that she may have known about it but I don't believe that she was involved," he said.