Tanvir Ansari, a doctor of traditional Indian medicine and a resident of the city, was led through a crowd of television reporters on Monday to hear the 11 charges against him in a court in central Mumbai.
A police inspector, Sunil Deshmukh, said, "We have arrested him on suspicion, for further interrogation. He has undergone training in Pakistan."
Among the charges facing Ansari are murder and violation of laws relating to explosives and the railways. He was remanded to police custody until August 4.
The chief of Mumbai's anti-terrorism squad said authorities believed Ansari had gone to Pakistan in 2004 where he learnt how to make bombs and the use of arms and ammunition.
"He is one of the key conspirators and we are assessing his role," K.P. Raghuvanshi told reporters.
Ansari's arrest follows those of three Indian muslim men last week on suspicion of being involved in the bombings.
Investigators say the Pakistan-based Islamist militant group, Lashkar-e-Taiba, and the Pakistani military spy agency, Inter-Services Intelligence, were the prime suspects in the case.