Croatia booked their spot as one of the 32 participants at Brazil 2014 with a 2-0 play-off victory over Iceland on Tuesday, but Simunic's celebration has drawn criticism.
Following the game, Simunic used a microphone to address the fans in Zagreb by shouting: "For the homeland". In response to Simunic's call, the fans said: "Ready!"
The call was used by the Croatian pro-Nazi puppet regime, the Ustashas, who ruled the state when thousands of people were killed in concentration camps during World War II.
Simunic, 35, was punished by Croatian public prosecutors on Thursday, who hit the defender with a €3,200 fine.
And he could now face further punishment from football's global governing body.
A spokesman for FIFA confirmed to Perform: "We can confirm that disciplinary proceedings have been opened concerning the case."
As yet, no charges have been levelled against Simunic.
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