Chaudhary has been sent to 12 days custody of NIA by the court in Panchkula, near Chandigarh, which is hearing the matter.
Singh, who was arrested from Chitrakoot along MP-UP border following intelligence inputs, is also suspected to be involved in the 2008 Malegaon blasts case, sources said in New Delhi.
Singh, who is one of the alleged conspirators in the Samjhauta case, was known as 'Swamiji' in Chitrakoot, they said.
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It is the fifth arrest in the case. The NIA has already arrested Kamal Chauhan, Aseemanand and Lokesh Sharma for their alleged involvement in the blast.
A huge explosion that ripped through Samjhauta Express near Panipat in Haryana on February 18, 2007 and a subsequent fire in the coaches had led to the loss of 68 lives and injuries to 12 train passengers, including women and children.
Amid high drama while being taken inside the Court for the in-camera proceedings, Pehalwan claimed before a group of mediapersons his involvement in planting the explosives, but after the court hearing ended, he retracted and told the journalists he had been taken into custody "under a conspiracy."
The initial investigation into the bomb blast was conducted by the Government Railway Police and Special Investigation Team of Haryana Police but subsequently NIA took over the case on July 29, 2010 following a directive by the Home Ministry.