Video footage shows the Australian-born Simunic taking a microphone to the field, amid celebrations after his side had qualified for the 2014 World Cup, and chanting with the fans.
The 35-year-old could be heard addressing the crowd: “For the homeland!”
The fans respond: “Ready!”
The chant is linked with the Croatian pro-Nazi regime, the Ustashas, who controlled the state during the Second World War.
However, Simunic was quick to deny his actions, saying: “Some people have to learn some history. I'm not afraid. I did nothing wrong.
"I'm supporting my Croatia, my homeland. If someone has something against it, that's their problem.”
FIFA and UEFA have had to fine the Croatian Football Association in the past after many of the country's fans used the chant along with a Nazi salute.
World football’s governing body has so far failed to comment on the situation.