JFA president Kozo Tashima told a news conference that caretaker boss Akira Nishino would not continue in the role after steering Japan to the knockout stages in Russia.
And after the Japan team was welcomed home by hundreds of flag-waving fans, Tashima appeared to take a veiled dig at commentators who slammed their tactics in their final group match against Poland.
Under orders from Nishino, the Japan players ran down the clock despite losing 1-0, knowing unless they picked up two yellow cards or Senegal equalised against Colombia in the other Group H game, they would go through.
"I want to thank all the people who said they hated Japan or wouldn't support Japan anymore," said Tashima.
"Thank you for your interest in us. There were positives and negatives but that's all part of creating a football culture in Japan."
Japan were knocked out in the last 16 after losing 3-2 to Belgium, who scored three goals in 25 second-half minutes to erase a two-goal deficit.
"I wanted to improve the team's chances by one percent," explained Tashima, who controversially axed former coach Vahid Halilhodzic two months before the World Cup.
"I asked Nishino to produce a small miracle so I'm very proud of the team's efforts. But I will not try to persuade him to stay."
With former JFA technical director Nishino stepping aside, former Germany coach Jurgen Klinsmann has already been linked to the job, along with former Arsenal manager Arsene Wenger.
Clearing up misunderstanding
"I've never personally felt disappointment like that before," said Nishino, referring to the heart-breaking manner of Japan's exit.
"I could never have imagined a scenario like that last 30 minutes."
Nishino noted that Japan had managed to win just one game -- a 1-0 victory over 10-man Colombia in their opening game.
But they twice came from behind to draw 2-2 with Senegal in their next match.
"The players dug deep and found that little bit extra we needed to be competitive at the World Cup," said Nishino.
"We knew we would have to take a few risks. The players showed incredible desire and really went for broke."
Japan captain Makoto Hasebe exploded the myth doing the rounds on social media that the players had cleaned the dressing room and left a 'thank you' note after their loss to the Belgians, crediting team staff.
"We wanted to make up for going out early at the 2014 World Cup," added Hasebe, who retired from international football after Japan's defeat in Rostov.
"People didn't really give us a prayer, but we were desperate to prove the doubters wrong."
Nishino tipped Japan to reach the knockout stage at the 2022 World Cup in Qatar.
"We've written a new page in history -- or perhaps half-a-page," he said. "But the future looks bright."