The Mexican, who was appointed in July last year, has come under the spotlight in recent months as part of a probe into his time in charge of Real Zaragoza, with investigations focusing on a La Liga clash against Levante in May 2011.
Japan have parted ways with 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 reporters.
"We have reached the decision to terminate the contract with coach Aguirre at this time."
Aguirre succeeded Alberto Zaccheroni following Japan's poor showing at the 2014 World Cup in Brazil.