Japan are scheduled to play their first group stage game in the World Cup against Colombia on June 19, followed by Senegal five days later and Poland on the 28th.
A former worldwide 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.
The JFA said it told Halilhodzic of its decision on Saturday with Nishino coming to the job after managing Gamba for 10 seasons; winning the league in 2005 and the Asian Championship League in 2008.
Nishino was the head coach of the Japanese Olympic team at the 1996 Atlanta Games in which it pulled off a stunning upset of Brazil. But in 2012 he wrote a newspaper column on "the thrills of attacking football", setting out an offensive style of play. "Nishino has seen the team more than anyone else and he will be our new manager", Tashima added.
The straight-talking Halilhodzic was also reported to have ruffled feathers in the dressing room with his no-nonsense approach. Association president Kozo Tashima cited "communication" problems in explaining the firing and said the Bosnian had lost the trust of his players.
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"We'll do everything we can to produce good results [at the World Cup]". And the JFA had been hoping Halilhodzic could create a similar breakthrough for Japan.
He guided them to the 2018 World Cup-their sixth consecutive qualification for football's biggest tournament-after they overcame the likes of Saudi Arabia and Australia to top Asia's qualifying Group B.
He once reportedly banned his players from smiling, and he found himself in trouble with authorities on two separate occasions after traffic accidents in 2015 and 2017.
"We'll do everything we can to produce good results (at the World Cup)".
However, it was not a smooth path through to the finals.
The Japanese qualified for the finals for the first time in 1998 and have been present at the World Cup ever since.