Siddibapa, a resident of Maqdoom colony in Bhatkal in Karnataka, was wanted on charges of conspiring to stage terror attacks at various places in India.
He is also said to be a distant relative of Indian Mujahideen chief in India Yasin Bhatkal, currently in jail.
From his base in Dubai, Siddibapa recruited Indians for the Indian Mujahideen and funded their activities, the official said.
A warrant of arrest and a Red Corner Notice had been issued against him, leading to his deportation.
Wahid was wanted for his alleged involvement in the July 2006 Mumbai serial blasts, the 2008 Delhi blasts and the 2010 Chinnaswamy Stadium blasts in Bangalore, according to an Interpol red corner notice.