Japan will face Colombia, Senegal and Poland in group play in the World Cup.
Nishino took the job as JFA's technical director in 2016, after managing J-League teams including Gamba Osaka and Nagoya Grampus in the first division.
The straight-talking Halilhodzic has made few concessions in Japan's famously polite society, and his style reportedly stirred tensions between the coach and the dressing room.
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.
The Sports Hochi daily said today "a sense of unity was lacking" between him and the team.
In 2010, Halilhodzic suffered a similar fate while at the helm of the Ivory Coast national team, helping them qualify for the World Cup and then being sacked just four months before the tournament. However, further criticism was to follow with poor performances and results in the eight matches played since qualification was secured.
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"Sometimes I'd really like them to be more aggressive, more street-smart, more vicious", said the former Nantes and Paris Saint-Germain striker.
However, pressure on the 65-year-old has been building and a draw with Mali and defeat to Ukraine in friendly matches last month did nothing to ease concerns about the team's form heading into the World Cup.
"We only have two months left until the World Cup, so the new manager had to come from within the organization".
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.
South Korea's run to the semifinals in 2002 as co-host remains the best run by an Asian team at the World Cup.
The Franco-Bosnian was one of the managerial successes of the 2014 World Cup as he guided surprise-package Algeria beyond the group stages with a series of impressive performances.
Halilhodzic, who recovered from being wounded in 1992 during the Bosnian war, insisted he was no "dictator" - but acknowledged his frank approach was capable of "wounding" some people in Japan.