Naqvi had publicly remarked that if men like Sabir Ali, who had alleged links with Indian Mujahideen militant Yain Bhatkal, could be inducted into the party, then Dawood Ibrahim could also be invited to join the party.
Naqvi's stinging remarks raised the heckles of the party leadership, with some senior RSS leaders also objecting to the induction of Sabir Ali.
Sabir Ali was inducted into BJP on Friday formally in the presence of party leaders J P Nadda and Dharmendra Pradhan.
Sabir Ali had been openly praising Narendra Modi for his leadership skills.