The victory ensured Zaragoza, coached by Aguirre at the time, avoided relegation. The prosecutor alleges the Levante players were paid a total of 965,000 euros to deliberately lose the game.
Aguirre has repeatedly denied any wrongdoing.
Japan Football Association official Hiromi Hara said the body's president Kuniya Daini had apologised at an executive meeting for "all the concern (the case) has caused for the players, sponsors and fans", Kyodo news agency quoted him as saying at a news conference.
But Aguirre would be allowed to stay in the role.
"The law in Japan and Spain is different, and we are gathering information as to what is happening and how this might unfold," Kyodo quoted Hara as saying.
"But at this stage, we are not thinking about the ifs and mights about Aguirre. This issue could turn in different directions. But at this point in time, Daini says Aguirre will be in charge at the Asian Cup. That is the current situation."
The investigating judge overseeing the Valencia case will rule on whether to proceed with prosecution.
Defending champions Japan open their tournament against Palestine in Newcastle on Jan. 12.
(Writing by Ian Ransom; Editing by ....)
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