Nishimura made a number of questionable decisions in the tie, culminating in the awarding of a controversial penalty – given against Croatia defender Dejan Lovren for an alleged foul on Fred - from which Neymar put Brazil 2-1 up.
Neymar was also lucky to escape a red card for an elbow on Luka Modric, while Croatia also had a goal from Ivan Perisic chalked off for what the referee deemed to be a foul on goalkeeper Julio Cesar by Ivica Olic.
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Busacca, however, felt the referee was entitled to give the penalty which changed the course of the game.
Speaking at Friday’s Fifa daily briefing, he said: “The referee is concentrating on the situation and the gesture [of Lovren putting his hands on Fred].
“How much was the gesture? How much was he really holding? Black and white is something we can discuss. Many say yes, many say no. It is important to keep your opinion.
“The referee had a very good position and from there he saw. On the pitch he has one second to make the decision.
“Unfortunately, the referee is not the defender or the attacker to understand or to know how much it was or was not [a penalty].
“We made it clear we did not want to see holding. There was contact. We are not here to discuss that. That’s why we are working on prevention.
“[He made contact] with the left hand and the right hand. If you make contact you permit the referee to go in one direction.”
Busacca refused to say whether Nishimura will miss any World Cup games on the back of his performance.
“It is impossible to say, we have not fully analysed his performance yet,” he added.
“The game is 90 minutes long, not just one situation.”