The agency had recently dispatched a clarification countering 12 apparent holes that the ministry had picked in its plea seeking sanction to prosecute Kumar.
The ministry had asked some pointed questions related to the CBI's theory of weapons being planted on the victims, testimony of witnesses and identity of those involved, among others.
It had also sought an explanation from the agency on its position regarding the chief of Ahmedabad police in the case.
The ministry and CBI have locked horns over the issues as the latter has refused to share the details of the case.
While IB, which comes under MHA, holds that the encounter -- in which Ishrat Jahan was killed along with three others by Gujarat crime branch personnel in Ahmedabad in June, 2004 -- was a genuine counter-terror operation, CBI believes otherwise.