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.
CBI sources said the agency did not provide any new details but had reiterated its previous position on all the points raised by the ministry while justifying the stand that there was a fit case for prosecuting Kumar over his alleged participation in the criminal conspiracy.
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 the Ministry of Home Affairs, 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.