The Pharaohs will host Botswana in the last round of the Africa Cup of Nations (AFCON) qualifiers.
The seven-time African champions held to a 1-1 away draw against Cape Verde in the fifth round on Friday.
According to a statement by the EFA, the 23-year-old Zamalek player Shehata sustained an adductor muscle during the Cape Verde game that will sideline him against Botswana.
Meanwhile, Ahly's El Shenawy, 35, and Al-Wakrah's Fathy, 30, will be serving a suspension after getting the second successive yellow card for each in Friday's game.
Against Botswana, Egypt will restore the services of key players such as in-form Eintracht Frankfurt's winger Omar Marmoush, who was rested by coach Hossam Hassan in Friday's draw.
Also, Ahly midfielder Marwan Attia and Al Rayyan's winger Mahmoud Trezeguet will be available after ending their one-match suspension.
Friday's result keeps Egypt, already qualified for the tournament, atop Group C with 13 points. Cape Verde, with only four points, are out of contention for a spot in next year's finals in Morocco.
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