The Chief Judicial Magistrate of Ajmer had issued a production warrant against Aseemanand on January 18 and the ATS has now brought him from the custody of National Investigation Agency in Panchkula, Haryana.
He was produced before Judicial Magistrate-I, Ajmer, Vikram Singh who remanded him to the ATS custody.
"We will interrogate him and will produce him in the court tomorrow," Additional Superintendent of Police (ATS) Satyendra Singh told PTI.
Aseemanand is accused in the dargah blast in which three persons were killed.
A Panchkula court had earlier on January 15 recorded the statement of Aseemanand in connection with the Samjhauta case. The blast in the Indo-Pak train in Haryana's Panipat district had left 68 people dead in February 2007.
Aseemanand was arrested by the CBI on November 19 last year for his alleged involvement in Mecca Masjid blast in Hyderabad that left nine persons dead. He was earlier living under a fake identity in Haridwar.
His name had also come up during the probe in Malegaon blast of 2008 when Maharashtra Anti-Terrorism Squad recovered the number of the Swami's driver from Sadhvi Pragya Singh Thakur, another Abhinav Bharat member and an accused arrested in Malegaon case.