Japan Football Association president, Kozo Tashima stated the reason for Halilhodzic sack to include lack of communication and weakened trust from players.
It was not the only big call he made in his spell in charge, dropping national team stars Keisuke Honda, Shinji Kagawa and Shinji Okazaki from the squad, and earning a great deal of criticism when starting Hotaru Yamaguchi of Cerezo Osaka - who were at the time playing in Japan's second tier.
"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".
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.
They begin the competition with a tough tie against Colombia on June 19, followed by encounters with Senegal and Poland to see out the group stages.
South Korea fired coach Uli Stielike past year and replaced him with Shin Tae-yong.More news: Stocks of Rusal collapse 50% after USA sanctions
More news: API shows fall in United States crude-oil inventories
More news: Smith, Bancroft won't challenge cricket ban
The head of the association praised Halilhodzic for helping Japan qualify for its 6th straight World Cup.
South Korea's run to the semifinals in 2002, when it was co-hosting the tournament with Japan, remains the best run by an Asian team at the World Cup.
Some Japanese football fans expressed shock and anger over the timing of the dismissal, fearing it could affect team preparations ahead of the World Cup.
Franco-Bosnian 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.
None of Asia's four representatives won a match at the 2014 World Cup in Brazil, all failing to advance beyond the group stage. Japan, South Korea and Iran each had one draw and two losses and Australia lost all three matches in a group containing the Netherlands, Chile and Spain.