Croatia players and manager Niko Kovac were furious after their 3-1 defeat in Sao Paulo.
The main bone of contention was referee Yuichi Nishimura's decision to award the Brazil a second-half penalty after a coming together between Dejan Lovren and Fred with the score 1-1.
That proved a turning point in the game, as Neymar converted from the spot before Oscar added a late third for the hosts, but FIFA have rubbished claims that the hosts are enjoying preferential treatment.
Thierry Weil, a spokesman for the governing body, said: "Here you are pretending something. I cannot let it stay like that. You are pretending FIFA is helping the host country which in my view is not the case.
"I have seen pictures from what happened; like Massimo (Busacca, the FIFA referees chief) said, it will be analysed. For sure here in the room you will have half say it was a penalty and the other half say it wasn't a penalty.
"We are talking here about a second of a decision, what the referee has to do. What we can guarantee you is that FIFA has nothing there to favour the host country."
Busacca, a former referee, added: "When you are on the pitch and you take a decision in one second, it is 'Team A' and 'Team B', 'Player A' and 'Player B'.
"You don't have time to think on the decision. You don't think, 'Aah I am in Brazil'. You do not have time - (it is) impossible."