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Aguirre, who took over as Samurai Blue boss in July, replacing Alberto Zaccheroni, left the national team camp on Monday to 'attend a ceremony in Mexico', according to the Japanese Football Association website.
Japan have a friendly against Honduras on Friday, with assistant coach Stuart Gelling taking charge until Aguirre's return on Thursday.
"It's rare that you don't have your coach, but it will be only for a few days, and with our coach or not, it won't change that the two games will still be important," AC Milan forward Keisuke Honda said.
"I think that we are going to have to brace up in working in our practices."
Aguirre meanwhile claimed he was close to deciding the first XI for the meeting with fellow 2014 World Cup side Honduras prior to his departure.
"I already have the starting members for the Honduras game in my head, but will make the final decision either on Thursday night or Friday morning," he said.
The brief absence of the head coach could prove to be a boost for Australia boss Ange Postecoglou as he looks to arrest the Socceroos' recent form slump.
Japan without coach Aguirre
