CSKA Moscow's Keisuke Honda and Inter Milan defender Yuto Nagatomo are among those who will play in Japan's first full internationals since the deadly earthquake and tsunami on March 11.
"We only have three more matches before the start of the World Cup qualifiers (in September)," Zaccheroni told reporters.
"So these two games are very important. Results are important but more relevant is the development of the team.
"Both the Czech Republic and Peru are aggressive and fight hard. These games will toughen us up," added the Italian, who is set to blood 19-year-old Gamba Osaka striker Takashi Usami.
"(Usami) is an Olympic player and has excellent potential. For a 19-year-old he already has a lot of ability."
Borussia Dortmund midfielder Shinji Kagawa is the only notable absentee after recently recovering from a fractured metatarsal suffered at the Asian Cup in January.
Chelsea goalkeeper Petr Cech will travel to Japan for the tri-nation Kirin Cup tournament despite fears over the nuclear crisis north of Tokyo.
Montenegro and New Zealand both pulled out of friendly internationals against the Asian champions at the end of March citing potential health risks posed by stricken power plant.
"At the beginning everyone was concerned," Cech told Japanese media. "But we have got all the (safety) guarantees."
Japan had wanted to use the Kirin Cup as a tune-up for their appearance at July's Copa America until they were forced to pull out as team's refused to release players.
The Blue Samurai face Peru in Niigata on June 1, the Czech Republic play the South Americans three days later, before Japan and the Czechs meet in Yokohama on June 7.
The disaster, which ravaged north-east Japan and ripped through a nuclear plant 150 miles north of Tokyo, has plunged sport into chaos across the country.
Despite Japanese assurances, several foreign teams and athletes have refused to travel to Japan because of fears over the risk of exposure to radiation.
Japan squad:
Goalkeepers - Eiji Kawashima (Lierse), Masaaki Higashiguchi (Niigata), Shusaku Nishikawa (Hiroshima).
Defenders - Yasuyuki Konno (FC Tokyo), Yuzo Kurihara (Yokohama), Masahiko Inoha (Kashima), Yuto Nagatomo (Inter Milan), Tomoaki Makino (Cologne), Michihiro Yasuda (Vitesse Arnhem), Atsuto Uchida (Schalke 04), Maya Yoshida (Venlo).
Midfielders - Yasuhito Endo (Gamba Osaka), Makoto Hasebe (VfL Wolfsburg), Kosei Shibasaki (Kawasaki), Ryota Moriwaki (Hiroshima), Hajime Hosogai (Augsburg), Akihiro Ienaga (Mallorca), Daigo Nishi (Kashima).
Forwards - Ryoichi Maeda (Iwata), Tadanari Lee (Hiroshima), Kunimitsu Sekiguchi (Sendai), Shinji Okazaki (Stuttgart), Keisuke Honda (CSKA Moscow), Shinzo Koroki (Kashima), Takashi Usami (Gamba Osaka).
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