The ATS had taken Shaikh Nayeem alias Sameer into their custody on April 24 from the BSF for his alleged involvement in the May 2006 arms haul, in which a large cache of arms and ammunition had been seized.
Nayeem, was produced before special MCOCA judge Mrudula Bhatkar on Monday where the ATS sought an extension of his police custody in order to carry out further investigations.
However, Nayeem told the court that the ATS officials had tortured him physically and sought that their plea be denied.
Judge Bhatkar then ordered that Nayeem be taken to a local hospital for a medical check-up to verify his claims and ordered that he be kept in judicial custody for one day.
The medical report is expected to arrive by Tuesday.
Nayeem was arrested in West Bengal by the BSF along with a Kashmiri and two Pakistani mercenaries while helping them cross over into India through the porous Indo-Bangladesh border and is suspected to have been in contact with the prime accused in the Aurangabad arms haul case.
Nayeem, a native of Aurangabad, has been booked under the stringent Maharashtra Control of Organised Crime Act.
A consignment of 43 kg of RDX, 16 AK-47 assault rifles and ammunition was recovered and 17 persons were arrested in the months of May and June 2006 from the Marathwada region for their alleged involvement in the case.