Yuji Nishida and Yuki Ishikawa both scored 23 points for Japan and Porya Yali had 13 points for Iran.
Team Melli has won four and lost five out of nine matches so far.
Iran national volleyball team will play Italy on Monday.
The 2019 edition of the FIVB Volleyball Men's World Cup features 12 national teams from the five continental confederations playing in Nagano, Fukuoka and Hiroshima in a round-robin format from October 1 to 15.
The Men's World Cup kicked off for five match days in Fukuoka and Nagano and the teams have moved to Hiroshima for the remaining six match days.