Jess Kavanagh-Williams crossed the whitewash for the hosts’ only points of the first half, which saw the visitors score four tries.
Despite promising signs in Wales’ attack, Japan added another five tries in the second half, before Wales finished the game on a high through a try from driving-line out, with replacement Kelsey Jones touching down for the score.
Rowland Phillips selected an inexperienced side for the clash at the CCB Centre of Sporting Excellence, as they continued preparations ahead of August’s World Cup campaign in Ireland.
The visitors made a strong start to the game and the early possession paid off as No 8 Mateitoga Bogidraumainadave powered over for her side’s first try of the afternoon.
Minori Yamamoto was off target with the conversion attempt, but her side quickly doubled their advantage, as a neat angle by Iroha Nagata sliced open the hosts’ defence, allowing the centre to slide in for the score.
Wales replied immediately, however, as Kavanagh-Williams exploited space on the outside to run in from 30 metres, but the conversion attempt from out wide fell just short of the posts.
A Welsh infringement in midfield saw Japan’s Mayu Shimizu convert a straightforward penalty to put her side eight points ahead.
Wales looked to bounce back immediately to narrow the visitors’ lead once again, but despite a period of sustained Welsh attacks, and numerous penalties conceded, Japan managed to turn the ball over and relieve pressure.
The visitors once again built up phases in the Welsh half and eventually created space for Akari Kato on the right to run in unopposed for her side’s third try of the half.
As the game entered the final play of the first half, Japan were camped on the Welsh 5m line, and after numerous phases, the pressure told as the forwards forced their way over to take the score to 5-23 at half time.
Japan picked up where they left off in the second half, as Nagata and Kato both secured their second tries of the afternoon, within the first 10 minutes, to give their side a 30-point advantage.
An up-and-under kick from inside the Wales 22m was collected by the covering Japanese defence, who quickly shipped the ball out wide.
Despite a scrappy pass as they neared the touchline, the ball still eventually found its way to Yui Shiozaki, who raced clear for her side’s seventh try of the game, before prop Saki Minami added another with 15 minutes remaining on the clock.
Wales looked to finish the game on a high, and after Bogidraumainadave was sent to the sin-bin, replacement Jones powered over from the back of a driving line-out to make it 10-45.
However, Japan had the final say as Yuki Oyokawa snuk through for a try in the final play of the game.
Wales will face Canada, Hong Kong and New Zealand in the World Cup pool stages, which will be held in Ireland in August.
Wales: Jodie Evans; Angharad de Smet, Elen Evans, Rebecca Defilipo, Jessica Kavanagh-Williams; Kayleigh Powell, Sian Moore; Gwenllian Pyrs, Morfudd Ifans, Megan York, Rebecca Rowe, Gwen Crabb, Lleucu George, Nia Elen Davies, Siwan Lillicrap
Replacements: Kelsey Jones, Catrin Edwards, Brea Leung, Amy Thomas, Mel Clay, Alisha Butchers, Bethan Lewis, Ffion Lewis, India Berbillion, Carly Jones
Japan: Mayu Shimizu; Akari Kato, Iroha Nagata, Makiko Tomita (C), Keiko Kato; Minori Yamamoto, Yumeno Noda; Makoto Ebuchi, Misaki Suzuki, Saki Minami, Aoi Mimura, Aya Nakajima, Yui Shiozaki, Ayaka Suzuki, Mateitoga Bogidraumainadave
Replacements: Chihiro Kobayashi, Mizuho Kataoka, Maiko Fujimoto, Sayaka Suzuki, Yuki Oyokawa, Moe Tsukui, Mizuho Ito, Chikami Inoue, Honoka Tsutsumi