Justice Mario Carroza said Wednesday there is insufficient evidence to try Fernando Matthei, the former commander-in-chief of the Chilean air force, The Santiago Times reported.
The judge said there was not enough evidence to show Matthei was aware of and participated in the torture and death of Bachelet.
Carrozo added two former generals are now being held who are known to have tortured Bachelet.
Eduardo Contreras, the attorney who requested the investigation of Matthei, said he would appeal the decision. He cited statements from 20 former officers who were tortured during the same period and who saw Matthei in the academy where he was in charge.
Contreras added Matthei admitted on public television he was aware of everything that happened at the academy.
Bachelet's widow has said she does not believe Matthei had a role in her husband's death because the two men were close friends.
Notable deaths of 2014 [PHOTOS]