The Mexican returned to his homeland on Tuesday to attend a ceremony, and he is due to be back with the squad before Tuesday's meeting with Australia.
Stuart Gelling will be in charge for Friday's meeting with Honduras in Toyota.
Aguirre is eager to get his team performing well in what is their penultimate friendly before next year's Asian Cup.
"We want to put up good results posing two wins this time, and want to complete the buildup of our team for the Asian Cup," he told the Japan Football Association website.
"I told our players to play boldly and for our new guys I told them to be part of this team as quickly as they could, and stick to the team disciplines.
"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."
Milan attacker Keisuke Honda said Aguirre's absence made the upcoming games no less important.
"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," he said.
"I think that we are going to have to brace up in working in our practices."
Japan are looking to bounce back from their 4-0 loss to Brazil last time out and they have been in indifferent form since the World Cup.
Honduras salvaged a draw against the United States in their previous match, and will be eager to trouble the hosts.
Even without Aguirre, Japan are likely to be too strong as they continue preparations for the Asian Cup.
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