The motorcycle blast killed six people and more 100 were injured.
On Saturday, the NIA had arrested one of his associates Rajendra Pehelwan alias Samandar from Nagda in MP.
"Singh was arrested from Chitrakoot in Satna district of MP. Samandar's questioning led to his arrest. Both Singh and Samandar were part of the core group of Hindu extremists who were behind a series of blasts in places such as Samjhauta train, Mecca Masjid, Ajmer Sharif and Malegaon. The NIA will question both of them together," senior home ministry official said.
Witnesses have told investigators that Singh had gone to Jammu for training along with Samandar in 2006 by their gang leader Sunil Joshi. Joshi, a former RSS prachark, was close to a senior functionary of RSS who runs some institutions in Jammu. Investigators hope that the arrest of Singh and Samandar might help them to unravel the role of senior RSS functionary who has been under scanner of the agency for last few years.
According to sources, Singh and Samandar were very close to Joshi who was murdered in December 2007. Singh was last spotted in June 2010. There after he went in hiding.