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Before the weather intervention, New Zealand established an early lead through a Dane Johnston try, created by breaks from Charlie Sinton and Micah Fale.
Japan responded via a maul try from Kise Shin, taking advantage of New Zealand's disciplinary issues after Mika Muliaina received a yellow card.
Shinnosuke Uchida scored from a kick-and-chase, and Sota Miura leveled the score at 21-21 before halftime.
New Zealand head coach Kane Jury selected midfielder Haki Wiseman as captain to lead a squad featuring All Blacks Sevens players Bradley Tocker and Kele Lasaqa.
"We’ve had a strong preparation here in Georgia and are feeling positive ahead of the first match.
Haki and the other leaders in the team have been great and are looking forward to getting the campaign under way," said Kane Jury, New Zealand Under 20s Head Coach.
The team adjusted to local conditions over the preceding week before facing their opening opponents.
"We’ve had a week to adapt to the heat and the facilities here in Georgia have been excellent.
We expect a tough first up match against Japan, who we expect to be very well drilled and play a fast-paced game, so we’ll need to be at our best," added Jury.
In the second half, Chris Boyd's side took control as Logan Williams and vice-captain Caleb Woodley scored tries before Muliaina added a final try at the 66-minute mark.
New Zealand holds six historical World Rugby Under 20 titles from 2008-2011, 2015, and 2017, and finished as runners-up in the 2025 edition.
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New Zealand's next scheduled Pool B matches are against Scotland on July 3 and Italy on July 7.
