Official sources said he was arrested and presented before a court in Ujjain in Madhya Pradesh which given the NIA his transit remand. Chaudhary carried a reward of Rs.5 lakh on his arrest.
The NIA was handed over the probe into the blasts 2010 and has already filed chargesheets in the case.
The bomb blasts in the Samjhauta Express took place near Panipat in Haryana Feb 18, 2007 in which 68 people died, many of them from Pakistan.
The Samjhauta Express (Attari Express) is a bi-weekly train that runs Wednesdays and Sundays between Delhi and Attari in India and Lahore in Pakistan.
The initial investigation into the bomb blasts in the Pakistan-bound train was conducted by the Government Railway Police and special investigation team of Haryana Police.
The arrest in the case has coincided with Pakistan Interior Minister Rehman Malik's visit to the country.
Malik in his remarks to the media has been talking of Samjhauta Express blasts in the same breath as the Mumbai terror attack of 2008. He also said there had been concern in Pakistan over the blasts in the train.
Sources said that the arrest sent a signal to Pakistan to act more decisively to bring to book those responsible for the Mumbai terror attack that killed 166 people.
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