
Kyodo news agency quoted JFA President Kozo Tashima as saying the Bosnian had been informed of the decision and his replacement would be announced at a news conference later in the day.
The timing of the decision means Halihodzic’s replacement will have little time to prepare for the World Cup, where Japan are drawn in Group H alongside Colombia, Poland and Senegal.
Japan have three friendly matches scheduled before opening their World Cup campaign against Colombia on June 19.
Halihodzic, who took over in March 2015, led the team to their sixth straight World Cup finals after they finished top of Asian qualifying Group B ahead of Saudi Arabia and Australia.
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.
Japan’s next warm-up game for the World Cup is against Ghana on May 30.