Playing for the final time at the National Stadium in Tokyo, which will be pulled down and rebuilt for the 2020 Olympic Games, Kagawa thrilled the home crowd by setting up the opening goal for Shinji Okazaki in the fourth minute.
Masato Morishige scored his first goal for the Blue Samurais in the 11th minute, heading in a free kick from Honda on the right before the AC Milan player backheeled a pass for Okazaki's second goal to give Japan a 4-0 lead.
"For the first 30 minutes, we played very well and were able to execute our game plan," Japan coach Alberto Zaccheroni was quoted as saying by the Kyodo news agency.
"After that, our pace slowed. New Zealand was a very good opponent for us."
New Zealand, who failed to qualify for Brazil after losing to Mexico in the playoffs, improved as the match progressed but the damage was already done.
Chris Wood lent some respectability to the result with a brace for the visitors, his first goal coming in the 39th minute and the second 10 minutes from time.
Wednesday's friendly was the last match before Italian Zaccheroni names his squad for the World Cup finals.
Japan, who were the first team to qualify for Brazil, are in Group C with Colombia, Greece and Ivory Coast.
- Sports & Recreation
- Shinji Okazaki
- David Moyes