Officials of the State Security Service (SSS) told PTI on condition of anonymity that the arrest was made possible by GPS tracking in the sect`s enclave of Maiduguri, in northern Borno state.
"We have finally picked Abu Qaqa up and he is currently in our custody, you can report that as a confirmed development," another official told the media in Abuja, the capital of Nigeria.
Qaqa has been speaking on behalf of the group, which has in recent times claimed responsibility for frequent bomb and gun attacks in northern cities and Abuja.
He was responsible for the issuance of all threats that came out from the hidden enclave of the sect, including the ones that preceded the bombings of the Police Force headquarters building, and the UN building -- both in Abuja.
According to security sources, Qaqa had not only been the spokesman of the fundamentalist group but was equally involved in coordinating several attacks and bombings.
An Indian named Kevalkumar Kalidas Rajput and his two Nepalese colleagues Hari Prasad Bhusal and Raj Singh were among the people killed by militants in the latest spate of deadly attacks in Kano city.
Boko Haram sect has been waging a bloody conflict in Nigeria, seeking to install an Islamic government and Sharia rule in the country.