Leon Angel is understood to have broken two of the governing body's rules regarding the role played by representatives in transfers.
He has now been asked to pay £4,654 for the alleged misdemeanor.
A statement from Angel's company read: "The breach of which he has been found guilty is a technical breach only and relates to the completion of paperwork in relation to a player transfer. No question has been raised as to Mr. Angel's integrity or honesty.
"Mr. Angel understands that another agent involved in the matter has also been sanctioned by FIFA but the governing body has chosen not to make this information public.
"Mr. Angel has requested an explanation for this apparent difference in treatment and is considering an official complaint."
Gomes joined Tottenham from PSV in 2008 for around £8m.