Fernandez announced major changes at the top of the military command structure just before she was hospitalized for treatment of thyroid cancer, which, for presidential loyalists, has soured the success of her landslide victory in elections last year.
The military reshuffle reinforced criticism that the president's preference for a strong concentration of power weakened Argentina's democracy and left the country ill-prepared for transition.
Fernandez aides say the president is fine after the surgery but panic over her health is seen likely to affect both politics and the economy.
The military shuffle was interpreted as part of Fernandez's aim to remove potential opponents in the military establishment and to clear the air after persistent reports of corruption and a scandal over the navy's surveillance and spying on politicians and other influential people.
Controversial navy chief Adm. Jorge Godoy, who was removed earlier and is facing criminal charges over the surveillance and spying, was replaced by Rear Adm. Carlos Alberto Paz, a veteran of the 1982 Falklands war with Britain.
Chief of Staff Operations commander Jorge Tellado would be replaced by Brig. Gen. Humberto Claudio Trisano, an official announcement said.
Another 12 army generals, 10 air force brigadiers and 13 rear admirals and vice admirals were ordered into early retirement the following day.
Fernandez and the military establishment have had a tense relationship most of the time since she rose to power in 2007. The main issues have been personnel pay, cash for military modernization and officers' reported unhappiness over having to report to civilians after many years of military dictatorship.
The uneasy relationship suffered more strains when the spying scandal broke in 2006. The navy faced a criminal investigation after a complaint launched by the Center for Legal and Social Studies, a think tank reported to be a victim of the spying and surveillance, and allegations by a young seaman who refused to take part in the spying activities.
A naval intelligence unit was found to be maintaining a hefty file on Nestor Kirchner, president of Argentina at that time and husband of Fernandez, who died in October 2010. The file indicated that the navy's spies had tracked Kirchner since the 1970s.
The government, the legislators and the media said the navy's spying operation was the military's answer to Kirchner's plans to bring to justice some of the perpetrators of the kidnapping, torture and murder during the 1976-83 dictatorship. Thousands of people perished in the military led campaigns against dissidents and suspected opponents of the dictatorship.
Godoy apologized in 2004 for the navy's part in the torture, killings and disappearances but failed to remove the stigma of distrust and guilt. The Argentine navy's Mechanical School was one of the major torture centers during the dictatorship.
Despite this week's reshuffles some key senior officers retained their posts. These include the armed forces Chief of Staff Brig. Gen. Jorge Chevalier, army commander Lt. Gen. Luis Alberto Pozzi and air force Chief of the General Staff Brig. Gen. Normando Costantino.