The African champions were held to a 1-1 draw by minnows Mauritania in the fourth round of their 2008 African Cup of Nations Group B qualifier in Nouakchott on Sunday.
The EFA sent CAF a fax asking that Egypt be awarded the three points because the game was held up for 40 minutes during the half-time break as the home fans invaded the pitch.
"Our players felt insecure and lost concentration because of what happened," EFA spokesman Medhat Shalabi told FilGoal.com on Tuesday.
"It’s an outrage," claimed Shalabi. "Even after the pitch was cleared, several spectators were surrounding the field, which was intimidating for our players who were not able to perform well in these circumstances."
Egypt are in charge of the group with 8 points, two ahead of second-placed Burundi who beat Botswana 1-0.