He appointed former defence ministry secretary general Mohammed Farid Hegazy to the post, it said, without giving a reason for the change.
His predecessor Mahmoud Hegazy, who had held the post since March 2014, was named a presidential adviser.
Linked to Sisi through the marriage of their respective children, Mahmoud Hegazy recently returned from Washington where military chiefs had gathered to discuss fighting "terrorism".
Mohammed Farid Hegazy's appointment is a major change in the military establishment.
Sisi came to power after the 2013 ouster of Islamist president Mohamed Morsi, for whom he had served as defence minister.
The insurgency is concentrated on North Sinai province, although IS has also extended its presence to southern Egypt and the Nile Delta, north of the capital.