The Mexican was appointed in August, but has come under the spotlight in recent months as part of a probe into his time in charge of Real Zaragoza.
Investigations are focusing on a Liga clash with Levante in May 2011.
Japan have taken the decision to remove Aguirre for fear of suffering repercussions in their bid to qualify for the 2018 World Cup.
"We came to think that we must avoid risks that these things affect the World Cup Asia qualifiers," Japan Football Association president Kuniya Daini told a news conference.
"We have reached the decision to terminate the contract with coach Aguirre at this time."
The decision comes after Japan turned in a disappointing performance at the 2015 Asian Cup.
Aguirre's side went into the tournament in Australia as defending champions, but were eliminated on penalties by United Arab Emirates at the quarter-final stage.
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