The visitors were in action for the first time since missing out on a place in the FIFA World Cup and subsequently seeing coach Ricki Herbert depart from his role.
However, caretaker coach Neil Emblen saw his side collapse under early pressure from the hosts as Japan moved four goals ahead inside 17 minutes.
Shinji Okazaki opened the scoring after just four minutes, Shinji Kagawa doubled the lead from the penalty spot and Masato Morishige got in on the act with his first goal for Japan.
Okazaki then completed his brace, but New Zealand demonstrated character in responding through Chris Wood, who struck late in each half to at least reduce the margin of his side's defeat.
Following their 9-3 loss over two legs to Mexico in November, New Zealand's hopes of beginning 2014 with a win were almost immediately dented when Okazaki took advantage of a lack of communication in the New Zealand backline to prod home.
Kagawa, who provided the assist for the opener, then converted a spot-kick after being felled in the area, before Keisuke Honda's free-kick from the right was headed home by Morishige.
A shellshocked New Zealand looked to reorganise but were hit with another hammer blow as Honda backheeled Kagawa's pass into the path of Okazaki, who finished well - although visiting goalkeeper Glen Moss will feel he could have done better.
The one bright spot for Emblen will be the spirit his side showed to pull two goals back - Leicester City striker Wood first threatening with a shot that hit the side-netting before curling a finish past Eiji Kawashima from a tight angle six minutes before the break.
Wood's second - a volley from inside the area 10 minutes from time - mattered little as Japan's preparations for the World Cup in Brazil got off to a positive start.
