Lt. Gen. Delfin Bangit was appointed to his position in March by outgoing President Gloria Macapagal Arroyo. He opted to retire early to avoid conflict with Aquino, who will become commander-in-chief when he is sworn in as president next week.
Aquino had said he would replace Bangit, who had headed Arroyo's presidential guard and was widely seen as a close ally of the president. His was one of a number of appointments Arroyo made in the final stages of her term that were seen as building a power base for after she left office.
"I am concerned that because of what happened to me, people would think the position of chief of staff is co-terminus (ends) with the commander-in-chief," Bangit said after a military parade in his honor at the main army base in Manila.
"This might lead our military leaders to allow political patronage or be lured to engage in partisan politics during an election period, perhaps out of fear that the change in government would make all his years of military service and accomplishments be taken for granted."
The military has played a pivotal role in Philippine politics over the past quarter century. In 1986, a group of soldiers mutinied against dictator Ferdinand Marcos, sparking a "people power" revolt that drove him from office.
In 2001, an army-backed popular uprising forced President Joseph Estrada from power over allegations of corruption.
Aquino's mother Corazon, president from 1986 to 1992, faced more than half a dozen coup attempts from rogue soldiers. Arroyo has also relied on loyal army generals to defend her government from three attempts by rogue troops to unseat her.
