The 63-year-old Nishino, who spent 10 seasons in charge of Gamba Osaka, was at the helm for one of Japanese football's greatest moments - a 1-0 win over a Brazil side containing Roberto Carlos and Ronaldo at the 1996 Olympic Games.
The JFA opted for Nishino because he was a former technical director of the Federation and possesses intimate knowledge of the national team and its set up.
A former global midfielder who won 12 caps for his country, Nishino is best known for his stint at the helm of Gamba Osaka and he took the club to their first Asian Club Championship in 2008.
A former global midfielder who won 12 caps for his country, Nishino is best known for his stint at the helm of Gamba Osaka, which he steered to the team's first Asian Club Championship in 2008.
Japan will play Colombia in its opening group stage match in June. "It's all about results in this game". Association president Kozo Tashima cited "communication" problems in explaining the firing and said the Bosnian had lost the trust of his players.
"I can't believe they are doing this just before the World Cup", said Yukina Muranaka, 29, a Tokyoite who is planning to travel to watch Japan play in Russian Federation, calling the decision "poorly planned".
In 2016, as Japan struggled to qualify for the World Cup, he told AFP he felt his players were too respectful.
"We only have two months left until the World Cup, so the new manager had to come from within the organization".
On Monday when the news of his departure was confirmed, the Nikkan Sports daily stated: "the association made the decision as it has a growing sense of crisis over the team's performance which has shown no sign of improvement with fewer than 70 days until the World Cup".
The tournament in Russian Federation will be the sixth successive World Cup appearance by the Blue Samurai, who made it to the last 16 in 2002 when Japan co-hosted the tournament with South Korea and again in 2010.
The nation shares a fierce rivalry with South Korea and such an admission of underperformance - alongside the result itself, a 4-1 defeat - ensured he was hounded by the national press.
Japan will be playing in its sixth consecutive World Cup and has only twice reached the knockout round - losing both times in the last 16.
However, the disappointing performance of the Japanese team in recent games, coupled with the team's dissatisfaction with the Bosnian coach, have pushed the JFA to terminate the contract with Halilhodzic.