Egypt defeated Guinea 1-0 in their opening Nations Cup qualifier (Ahram)
Although Egypt usually play at the 86,000-capacity Borg El-Arab Stadium when they host their games in Alexandria, the Malawi match will take place at a much smaller venue in September.
Alexandria Stadium, where the city's biggest team Ittihad host their matches, can accommodate up to 20,000 spectators. The EFA provided no explanation for its choice.
Egypt host the majority of their matches at either Cairo Stadium, the traditional venue of the national team -- which has a capacity of 74,000 fans -- or Borg El-Arab.
Attendance in the Egyptian Premier League is severely restricted, with only 5,000 fans currently allowed at a game. However, such restrictions are usually lifted for the Egyptian national team.
"The EFA has agreed to stage Egypt's Nations Cup qualifier against Malawi at Alexandria Stadium with full attendance after coordinating with security bodies," the EFA said in a statement.
Egypt have made a disappointing start to their Nations Cup qualifying campaign.
The record seven-time African champions scraped a 1-0 home win over Guinea in their opening Group D game before suffering a stunning 2-0 loss to Ethiopia in Malawi.
A 4-1 defeat by South Korea in a friendly led to the sacking of coach Ehab Galal after just three matches in charge. The EFA is looking for a foreign replacement, with local reports saying that Portuguese manager Paulo Sousa and Swiss Vladimir Petkovic had turned down offers to take charge of the team.
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