The Netherlands coach claims the decision to have Group B matches kick off ahead of Group A fixtures lends a helping hand to host Brazil.
The Oranje have already qualified for the knockout stage following victories over Spain and Australia and face Chile on Monday in a noon ET kickoff hoping to clinch the top spot in Group B.
Their next opponent will come out of Group A, where Brazil, Croatia and Mexico are vying for qualification, with that pool's final matches kicking off at 4 p.m. ET.
The Dutch coach sees the scheduling as favoritism toward Brazil, which has played its games prior to Group B matches over the previous two matchdays, and believes that the world governing body has been unfair to his side.
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"FIFA, for every match, has all their commercials and clips about fair play. But the way they play these tricks and schedules Brazil matches like this is not fair play anymore," Van Gaal said. "We're going to focus on a victory against Chile. I don't think that will be affected because Brazil play after us. We just expect they'll do their sporting duty."
Van Gaal has also heaped pressure on referee Bakary Gassama, who will be officiating a World Cup finals fixture for the first time Monday.
While he says he has not seen the 35-year-old in action before, Van Gaal is eager to see an improvement from his side's first two matches.
"I'm not going to give you an opinion on him as I've never seen him at work, so I assume FIFA have selected an excellent referee," Van Gaal said. "We have been awarded penalties against us very harshly twice, and that could have affected our qualification. It is unbelievable what my team has been able to achieve given that we have twice gone behind through incorrect penalty calls. Perhaps this referee will do a better job. I'm just hoping that FIFA has carried out a good selection policy."
The Dutch go into their final group fixture without suspended skipper Robin van Persie and injured defender Bruno Martins Indi, but the coach declined to reveal who might take their places or add any information on further doubts.
"There are a number of players who have been [injured] and one has been suspended. I'm not going to discuss individual players because I don't want the opponents to know what they want to know. Somehow when we have a closed training session, Dutch media find out what happens and I am not happy about that."
The match between the Netherlands and Chile at Arena Corinthians in Sao Paulo will decide the winner of Group B, with both teams having collected maximum points so far.