With the score tied at 1-1 in the second half, the referee awarded Brazil a penalty when Fred went down in the box, however, it was a contentious decision as there was very little contact on the striker.
As debate raged on about the decision, Merk, a former FIFA referee, launched a scathing attack on world football's governing body, insisting Nishimura should not have been put in charge of the crucial opening game of the tournament.
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"It is the World Cup, the opening match, that will never do! I am sorry, as a footballer, it even hurts me," he told Goal. "Croatia were fantastic, they have had a great opening game. But this penalty, in such an important match, that will never do!
"The Japanese referee is the least to blame. He is really a good one, who should by all means be allowed to referee at a World Cup. But not to set new standards, not in the first game of a World Cup. With lack of experience and worse, without instruction. I can't remember a referee who escaped after his whistle. Embarrassing! Don't criticize the Japanese referee, question FIFA and its commissions."
Meanwhile, former Thai referee Pirom An-Prasert, who officiated during the 1998 World Cup, says he doesn't think there was any issue with the referee's performance.
"Overall, the Japanese referee does a good job, all errors are minor," he told Goal. "To me there's no seriously bad call.
"For the penalty, he has the right to give it. It's a by-the-book penalty kick which he has given as the rule is obvious - if you interfere with an opponent's possession in the box, then the penalty can be given, no matter how hard or how light the touch is. That depends on the referee's discretion.
"Mr Nishimura's performance is on par in my view. The game runs smoothly as he tries not to interrupt the flow, which some may not like if they are used to referees who pause the game every chance they get."