Supporters held up cards to form poppy mosaics in the stands before Northern Ireland's match at home to Azerbaijan on Nov. 11 and Wales' game with Serbia the following day.
Players also wore black armbands.
Soccer's governing body said its disciplinary committee had opened proceedings against the Northern Irish and Welsh FAs "in relation to several incidents involving the display of signs."
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The laws of the game, drawn up by the International Football Association Board (IFAB), state that players' kit "must not have any political, religious or personal slogans, statements or images."
Jonathan Ford, chief executive of the Welsh FA, said they were "disappointed and surprised" by FIFA's action.
"Our intention was to show respect on Armistice weekend which we feel we did in the right and proper way.
"We also adhered to the rules and regulations of the competition and the communication from FIFA prohibiting the FAW request for the players to wear the poppy symbol on the armbands or the field of play."
The FAW website listed the reasons for FIFA's action, including "supporters in the stand wearing the poppy" and "a member of the armed forces holding a bunch of poppies at the exit of the tunnel".
The IFAB includes representatives of each of the British football associations and four representatives from FIFA.
FIFA has already opened disciplinary proceedings against England and Scotland after they wore poppies on black armbands in their Nov. 11 qualifying match at Wembley.
(Writing by Brian Homewood; Editing by Ken Ferris)
