The ATS sought the custody of the trio contending their interrogation was needed to find out the "sinister design of Hindu radical group Abhinav Bharat, which appears to be instrumental in promoting, advocating and inciting unlawful and terrorist activities".
However, Special MCOCA Judge Y D Shinde rejected the ATS plea and instead sent them as also four other accused in judicial custody till December 3.
All the seven accused produced before the court today alleged they were physically and mentally tortured by ATS while they were in its custody.
Clad in an saffron outfit with vermilion on her forehead, sadhvi Pragya Singh Thakur told the court that she has been mentally and physically harassed by ATS.
"ATS officials threatened to strip me and hang me upside down if I did not confess about my involvement in the blast. I am mentally disturbed and not able to eat anything," Sadhvi told the judge.
Purohit said he had been hung upside down from a rod and his hands were tied to two poles due to which he has lost sensation from his wrist to his fingers.
"ATS while questioning me said that it would plant RDX in my house and that it would be very easy for it to kill me in an encounter," Purohit told the court.
Another accused and retired army officer Ramesh Upadhyay alleged he was tortured by Additional Commissioner of Police (ATS) Parambir Singh and Sukhwinder Singh in custody.
"Parambir and Sukhwinder physically abused me and then threatened to parade my wife and daughter naked in the police station and get them raped by all the officers here," Upadhyay said.
The sadhvi and Purohit filed an application before the court seeking to be sent for medical examination in order to prove that they had been tortured in custody by ATS.
Special public prosecutor Rohini Salian argued that the source from where the explosives came and if money for them was obtained through hawala needs to be probed through interrogation of the sadhvi, Purohit and Rahirkar.
Sadhvi's advocate Ganesh Sonavi, however, argued that the only connection she has with the September 29 Malegaon blast is the vehicle used in the bombing.
"Apart from the vehicle, which was sold to someone else by the sadhvi much before the blasts, ATS has no evidence to connect Sadhvi to the blast," he argued.
Purohit's advocate Shrikant Shivade argued police custody is sought only for torturing the accused and forcibly extracting a confession from them.
The court will tomorrow pass an order on whether a probe needs to be initiated into the allegations levelled against ATS officials by the arrested accused.
Accepting the defence lawyers arguments that further custody of the accused would not be required, the court remanded the seven accused to judicial custody.
Eleven persons have so far been arrested in connection with Malegaon blast and all of them were booked under stringent Maharashtra Control of Organised Crime Act (MCOCA) last week.