Police arrested 35 Poland fans and one England supporter after the FIFA World Cup qualifier earlier this month, which Roy Hodgson's side won 2-0 to secure their place at the finals in Brazil next year.
Sixteen of those held were for use of flares and the world governing body has now confirmed that they are investigating the incidents that took place at Wembley.
A FIFA statement read: "We can confirm that disciplinary proceedings have been opened against The Football Association and the Polish Football Association for incidents that were reported during the preliminary competition match of the 2014 FIFA World Cup Brazil between England and Poland on 15 October 2013.
"As the proceedings are on-going, please understand that we cannot comment further."
England won the game courtesy of goals from Wayne Rooney and Steven Gerrard to qualify top of Group H.
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