Aguirre was among 41 people named by Spain's anti-corruption prosecutor, who filed its case in a Valencia court on Monday following a probe into Real Zaragoza's 2-1 win at Levante on the final day of the 2010-11 campaign.
The victory ensured Zaragoza, coached by Aguirre at the time, avoided relegation.
The prosecutor alleges that the Levante players were paid a total of 965,000 euros (766,751 pounds) in cash to deliberately lose the game with the Mexican named as one of three people who distributed the money to their opponents.
Aguirre has repeatedly denied the claims, and on Monday said he was not concerned about the long-discussed case after naming his 23-man squad for the Jan. 9-31 tournament in Australia.
"At the Asian Cup I will just be concentrating on the sports and competition side of things," he told reporters.
But with the prosecutor's filing coming hours later, uncertainty arose about whether the JFA might be tempted to temporarily -- or permanently -- remove the coach they only appointed in July to avoid the situation overshadowing them at Asia's biggest football tournament.
TWO-HOUR MEETING
Many fans of the Blue Samurai, a record four-times Asian champions, took to social media calling on the former Atletico Madrid and Mexico coach to be stood down.
Attempts by Reuters to contact the JFA on Tuesday went unanswered.
Earlier this month, the Mexican and his lawyer had a two-hour meeting with the JFA and their lead attorney Yutaka Miyoshi about the case.
The Kyodo News Agency reported that Miyoshi "learnt of nothing that could link Aguirre to the allegations" after the Mexican had told him: "I am a professional coach and I have never, ever done anything of the sort."
The seemingly positive outcome for Aguirre came with a caveat, though.
"This is anything but the end of it," Miyoshi said at the time. "If new facts do come to light, we will make a judgement. We will see how the investigation unfolds and respond accordingly."
Following Monday's developments, the next move will be to see if the investigating judge overseeing the Valencia case will proceed with prosecution.
Miyoshi had said he was told previously by Aguirre's lawyer that if the Mexican was prosecuted he could be ordered to appear in court in February.
That would fall after the Asian Cup but gives no reassurance that Aguirre will be in the dugout when Japan open against rank outsiders Palestine in Newcastle on Jan. 12
($1 = 0.8025 euros)
(Writing by Patrick Johnston in Singapore; Editing by John O'Brien)
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