Egypt led 2-0 with 11 minutes remaining of the regulation 90 minutes as well as stoppage time.
But Argentina skipper Lionel Messi set up one goal and scored another as his side returned from the brinkto win 3-2 at the Atlanta Stadium.
The EFA said it could not remain silent about what it considered unfair and biased decisions.
“Defending the rights and interests of the Egyptian national team is not a matter that can be ignored, minimised, or treated as secondary,” the EFA said in a statement.
“It is a responsibility that we carry with full conviction and determination.”
Egypt coach Hossam Hassan and several players complained about the referees in the wake of the defeat.
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They pointed to a disallowed goal in the 58th minute in which a video assistant referee (VAR) review determined that Marwan Attia had fouled the Argentina defender Lisandro Martínez before Mostafa Zaki Abdelraouf scored.
There was also a complaint that Mohamed Salah was fouled in the Argentina penalty area before the South Americans went on a counter-attack and scored their third goal.
Egyptians question fairness of decisions
The EFA statement said that the referee failed to use the VAR system appropriately, leading to the loss.
“Several key incidents raised serious concerns and left profound questions about the consistency and fairness of decisions that directly influenced the course of the game,” the statement said.
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Towards the end of the game as tempers flared, Hassan held his arms up in an “X” shape to signal racial abuse after Argentina's scored their third goal.
Egypt's goalkeeping coach Saafan Elsaghir was red-carded and several yellow cards were dished out to Egyptian players.
"Every player who wears the Egyptian shirt, and every supporter who stands behind the team, deserves fairness, respect, and equal application of the laws of the game,” the EFA statement added.
'Not watching matches'
After the game, Hassan said his team was the victim of a soccer establishment that favoured Messi and Argentina.
"From the moment I go back, I'm not going to continue following the matches of this World Cup," said the former Egypt international.
"This is my internal fight, my internal objection, my own way of speaking up and standing up. I am not going to watch not a single match of this tournament."
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During its fourth trip to the World Cup, Egypt reached the knockout stages for the first time after finishing second behind Group G winners Belgium.
Egypt beat Australia in a penalty shootout following a 1-1 draw in the last-32 before going down to Argentina.



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