Ajit Pawar said he would clarify his stand after Malik takes his own decisions.
In his letter to Ajit Pawar, who too is a deputy CM, Devendra Fadnavis said former Maharashtra minister Nawab Malik has the right to attend the assembly as an MLA.
The controversy erupted after Malik, out on medical bail, attended the first day of the winter session of the state assembly sitting in the treasury benches.
Earlier in the day, a special court set his bail conditions, one of which barred him from talking to the media.
Both the factions of the NCP celebrated the release of Nawab Malik by bursting crackers distributing sweets at their respective party offices in Mumbai.
Malik was arrested in February 2022 by the ED in the case allegedly linked to the activities of fugitive gangster Dawood Ibrahim and his associates.