Halilhodzic is already facing a humiliating performance review after Japan drew 1-1 with Iraq in an Asian World Cup qualifier.
The 65-year-old's car collided with another vehicle in Tokyo on Thursday afternoon, his second fender-bender in two years after running into a taxi in August 2015.
"We deeply apologise for the trouble this incident caused," Japan Football Association chief Kozo Tashima told reporters.
"We are relieved it wasn't serious and no one sustained injuries. We have warned the coach once again to take care when driving."
Halilhodzic is already facing a humiliating performance review after Japan drew 1-1 with Iraq in an Asian World Cup qualifier earlier this week.
The Franco-Bosnian's previous prang also followed a series of poor results, coming after Japan finished last at the 2015 East Asian Cup.
Halilhodzic has split opinions since taking charge following Japan's quarter-final exit at the 2015 Asian Cup.
The firebrand former Algeria coach has clashed with Japan players and staff in a rollercoaster two years.
Japan should still qualify for the 2018 World Cup but defeat against Australia on August 31 would put them at risk of dropping into a play-off.