Winger Jess Kavanagh-Williams’ try was Wales’ only score in a first half that saw coach Rowland Phillips’ side trail 23-5 at the break.
The Sakura 15s continued where they left off in the second half, as Nagata and Kato both grabbed their second tries within the first 10 minutes to give their side a 30-point advantage.
Yui Shiozaki and Saki Minami added their names to the scoresheet before Japan lost Bogidraumainadave to the sin-bin. Wales capitalised on their numerical advantage to score through Kelsey Jones, but Yuki Oyokawa ensured Japan had the final say with their ninth try right at the death.
With the three full rating points awarded to them for victory taking their total up to 64.32, Japan have now moved above the Netherlands, Portugal and Kazakhstan to a new high of 14th place in the rankings. Wales drop one to 10th as a result of the heavy loss on home soil with Italy the beneficiaries.