Croatia's coach and players erupted in fury at Nishimura's decision to award a penalty against defender Dejan Lovren for a foul on Brazilian centre forward Fred on Thursday night. Croatia coach slams referee after opening game defeat (JPN/Agencies)
Television replays indicated that Lovren barely touched Fred. Croatian media called it an "inexcusable mistake".
A top Brazilian newspaper used a front page headline "arigato" -- thank you in Japanese. Social media in Japan lambasted Nishimura's action, while World Cup players said that more and more of their counterparts would try to get away with such penalties.
FIFA defended Nishimura, but it said no decision had been taken as to whether he will appear in another match at the tournament.
FIFA referees chief Massimo Busacca insisted Nishimura had been justified in awarding the spot-kick.
"He had a very good position," said Busacca, referring to a photo of the incident which appeared to show Lovren's hands making contact with Fred.
"When he saw the hands doing something he makes it (the decision)," he said.
Nishimura, 42, has twice been voted referee of the year in Japan's J-League and was at the 2010 World Cup finals. But he has a reputation for controversial decisions.
But no sooner had referees chief Busacca sprung to Nishimura's defence then the standard of officiating was again under scrutiny as Mexico took on Cameroon.
Mexico's Oribe Peralta scored the only goal of a rain-lashed Group A game in Natal, securing a precious three points for Miguel Herrera's side.
But the main talking points after the game was the standard of officiating, with Colombia referee Wilmar Roldan chalking off what looked like two valid Mexico goals in the first half.
Furious Croatia coach Niko Kovac blamed "out of his depth" referee Yuichi Nishimura and warned the World Cup could turn into a circus after a contentious penalty decision effectively cost his team the opening game of the tournament against Brazil.
Japanese ref Nishimura ruled that Croatia's Dejan Lovren had fouled Fred when the Brazilian fell to the floor with 20 minutes remaining and the score at 1-1. Neymar converted the penalty for his second goal of the game and they went on to win 3-1 in Thursday's Group A match.
"This was ridiculous today, and if we continue in this way we will have a circus," Kovac told a news conference dominated by questions about the penalty.
"If that's a penalty, we don't need to play football anymore. Let's play basketball instead. The lads played their hearts out but that was outright thuggery by a referee who was just out of his depth for a game of this magnitude," he said.
Kovac, who said his team deserved at least a draw from a match played at a packed Corinthians arena in Sao Paulo, also felt Oscar's third goal near the end of the game should not have been allowed due to a foul earlier in the move.
"Was there a foul on my player? Yes. It was a foul. But that's life. We will march on. We will not be swayed,” he said.
Kovac, stony-faced yet calm, praised his team, which took the lead in the 11th minute after an own goal by Marcelo, and had several scoring chances during the rest of the match.
"My lads have fought for two years to reach the World Cup. They worked hard, prepared, and then they were faced with such a penalty decision here. You can imagine walking into our dressing room - what kind of mood my lads are in."
Kovac said he did not blame Fred for his theatrical fall. "The referee was well-placed, he was not unsighted, he saw everything and he took that decision," he said. "I don't blame Fred at all."
Croatia's fans were also furious with the Japanese official.
"I'll never eat sushi again," said Goran, a Croatian fan who attended the game as he ate dinner afterward. "I guess the world was against us today."
Despite the setback, Kovac said he remained confident his team could progress from the group. They play Cameroon in the hot and humid Amazon city of Manaus on June 18 and Mexico in Recife five days later.
"I am optimistic," he told Croatian television. "Naturally the lads are a bit down after this, but we will be up again as soon as we've had something to eat. We just have to make our way into the knockout stages because we are definitely good enough," he said.
Kovac said he looked forward to welcoming back Mario Mandzukic into the team for the next two games, after he was suspended for the opening encounter.
Croatia's coach and players erupted in fury at Nishimura's decision to award a penalty against defender Dejan Lovren for a foul on Brazilian centre forward Fred on Thursday night.
Croatia coach slams referee after opening game defeat