A statement released by the FA alleged the Super Blues player's Twitter message "was improper and/or brought the game into disrepute".
The tweet, which is understood to have been posted a number of weeks ago, has since been deleted.
“Emmanuel-Thomas denied the charge and requested a paper hearing. However, at an Independent Regulatory Commission hearing the charge was found proven," the statement said.
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The 22-year-old is reportedly in talks to move to Bristol City.