FIFA said the charge against the Croatian soccer federation was "due to the behaviour of its fans" and cited rules relating to discrimination and security at games.
Canada goalkeeper Milan Borjan was born in an ethnic Serb region of Croatia that was part of the conflict that split the former Yugoslavia in the 1990s.
Borjan's family left their hometown in 1995 when it was taken by Croatian forces amid stories ethnic Serbs fled on tractors.
During Canada's 4-1 loss on Sunday, one banner displayed by Croatia fans used a flag of tractor manufacturer John Deere and changed the marketing slogan to target Borjan.
Borjan moved as a child with his family to Canada and chose to represent that country at soccer, though he plays for storied Serbian club Red Star Belgrade.
FIFA gave no timetable for a verdict in the case which would typically be judged with a fine for the federation.
In the first disciplinary verdict of the World Cup on Tuesday, FIFA imposed a 10,000 Swiss francs ($A15,500) fine on the German soccer federation for not bringing players to the news conference that is mandatory one day before a game.
Coach Hansi Flick appeared alone Saturday in breach of tournament rules to meet international media in Doha ahead of the team playing Spain.
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