CAF Secretary-General Hicham El Amrani has also been charged.
With CAF based in Cairo, Egyptian authorities maintain it is governed by local laws.
The African football body firmly rejects accusations it committed any wrongdoing when signing a multi-million dollar deal with sports agency Lagardere in June 2015.
“CAF categorically asserts that all claims against it are groundless and without merit,” a statement read.
“CAF will vigorously defend its position, its right and reputation using all legal means available under international law.”
The Egyptian Competition Authority started to investigate the Lagardere deal in June 2016, prior to asserting – in January 2017 –that CAF had engaged in monopolistic practices that infringed local laws.
The deal gives Lagardere rights to a variety of African football competitions, including the flagship Africa Cup of Nations, from 2017 until 2028.
“As a result, the board voted in favour of (referring) Hayatou and El Amrani for criminal prosecution,” said the ECA in a statement dated March 8.
Caf stresses that the allegations accusing it of selling rights without opening them for due tender are incorrect.
The organisation, which celebrates its 60th anniversary this week, maintains it did not sell any broadcast rights to Lagardere – merely appointing the French company as its marketing and media agent instead.
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