Maysam Salehi earned 20 points for Iran and Nishida, Ran and Ishikawa seized 14 points each for Japan.
Iran will face Brazil on Thursday.
16th-placed Iran will also take on both 14th-placed Bulgaria on Friday and 15th-placed Turkey on Saturday.
The VNL Preliminary Phase features three competition weeks per gender, with each of the 16 teams playing 12 matches. The seven best-ranked national teams in the Preliminary Phase will join hosts Poland for the Finals, which will be held in Lodz from June 27 to 30.