Jones, the former Australia coach, has kept faith with the majority of the players that helped Japan claim a sixth successive Asian Five Nations title earlier this month, but has also added Shota Horie, Fumiaki Tanaka and Michael Leitch, who have been on Super 15 duty.
Jones said: "After the successful Asian 5 Nations, we have now picked a squad that we believe can win the Pacific Nations Cup and beat Wales, and we're looking forward to having Horie, Leitch and Tanaka back in the squad after the Super Rugby."
Japan begin their Pacific Nations Cup campaign against Tonga later this month and then face Fiji before hosting Wales in two Tests on June 8 (Osaka) and 15 (Tokyo). They then complete their PNC tournament against Canada and the United States.
Forwards: Yusuke Nagae, Masataka Mikami, Takuma Asahara, Shota Horie, Takeshi Kizu, Yusuke Aoki, Hiroki Yuhara, Hiroshi Yamashita, Kensuke Hatakeyama, Shoji Ito, Hitoshi Ono, Shinya Makabe, Justin Ives, Ryuta Yasui, Michael Broadhurst, Michael Leitch, Hendrik Tui, Takashi Kikutani, Ryu Koliniasi Holani.
Backs: Atsushi Hiwasa, Fumiaki Tanaka, Keisuke Uchida, Kosei Ono, Yu Tamura, Harumichi Tatekawa, Craig Wing, Ryoto Nakamura, Male Sau, Seiichi Shimomura, Yoshikazu Fujita, Toshiaki Hirose, Yuta Imamura, Hirotoki Onozawa, Kenki Fukuoka, Ayumu Goromarud.