Shehata leaves struggling Egypt
Egypt have not won a match in their group and were all but eliminated from the competition after Sunday's 0-0 draw.
Samir Zaher, head of the Egyptian federation, said in a statement that: "the federation has full respect for the management team over the past six years in terms of accomplishments."
Shehata led Egypt to the last three Nations Cup titles as well as bringing the team one of its highest FIFA rankings ever. Egypt were ranked ninth internationally last June but have since fallen to 36th position.
The federation did not name a successor to Shehata. Egypt still has two qualifying matches to play against Sierra Leone and Niger.