But he played the full 90 minutes as his team again lost 0-1 to Portugal in Moscow on Wednesday, a result that ended the African side's chances of advancing to the tournament's knockout stage.
"Following the questionable handling of the concussion incident involving the Moroccan player Amrabat during the Morocco-Iran match, FIFA wrote to the Moroccan team doctor to remind him of the importance to adhere to the guidelines that have been communicated," FIFA said in a statement.
"While the assessment and case management of concussion incidents falls under the sole responsibility of the respective team doctors, FIFA will address this matter with the Moroccan FA and, speaking in general terms, FIFA will monitor closely this matter throughout the competition," it added.
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FIFA guidelines recommend a minimum rest of six days for players who suffer concussion. After Wednesday's match, Morocco manager Herve Renard described Amrabat as a "warrior" and said the team's medical staff had deemed him fit to play.