Chaudhary, who is in his mid-30s, was arrested by the National Investigation Agency (NIA) last night from Nagda, 50 kilometres from Ujjain, where he was living under an assumed name, they said.
The sources said Chaudhary, who is also known as Samundar Singh among the right-wing extremists, had changed his complete identity and had been living under the assumed name for the last three years after NIA had announced a cash reward of Rs five lakh for his arrest.
They alleged that he was also involved in planting a bomb at Mecca-Masjid in Hyderabad on May 18, 2007 in which nine people were killed. Five more died thereafter in clashes with the police. A cell phone-controlled pipe bomb had gone off at the historical Masjid during Friday prayers.
NIA was handed over the case in 2011 after which the agency chargesheeted five persons -- Assemanand, Lokesh Sharma and Davinder Gupta (all under arrest) and Ramji Kalsangre and Sandeep Dange (both absconding).
Chaudhary would be questioned about his role in the blast cases as the probe has indicated that the planter of the bombs in Samjhauta Express and Mecca Masjid was the same, the sources in the probe agency said.
The breakthrough came after intense investigation being carried out in the case by the NIA which was handed over the Samjhauta probe in 2010 as they had mounted the surveillance on the accused after getting a tip off from informers that he was living under assumed name, the sources said.
It is the fourth arrest in the case. The NIA has already arrested Kamal Chauhan, Aseemanand and Lokesh Sharma for their alleged involvement in the blast.
Explosion ripped apart the Samjhauta Express near Panipat, Haryana, on Feb 18, 2007 and the consequent fire in the train coaches had resulted in the loss of 68 lives and injuries to 12 train passengers, including women and children.
The initial probe into the bomb blast was conducted by the Government Railway Police and Special Investigation Team of Haryana Police and subsequently NIA took over the case on Jul 29, 2010 following a directive by the Home Ministry.
NIA had on Jun 20, 2011 filed a chargesheet before the special court under various sections of the Indian Penal Code and Unlawful Activities (Prevention) Act against five accused -- Naba Kumar Sarkar alias Swami Aseemanand, Sunil Joshi (now dead), Lokesh Sharma, Sandeep Dange and Ramchandra Kalasangra alias Ramji.
The investigating agency had in August this year also filed a supplementary chargesheet in the case against disgruntled RSS worker Kamal Chauhan and his associate Amit in a special court at Panchkula charging them with murder, conspiracy and other offences.
Lokesh Sharma, a close associate of late Sunil Joshi, had sent Chauhan and Chaudhary for the recee in Dec 2006.
Later, Old Delhi railway station was selected (for planting bomb) from where the train originates, the sources said.
The Samjhauta Express was chosen as the target and both of them came to Indore on Feb 17, 2007 and took delivery of the suitcase bombs to be planted in the train on the next day.