Fernandez has been battling rising inflation and a drop in U.S. dollar holdings that has forced her administration to clamp down on imports.
The import curbs in turn have hit industrial productivity. Businesses involved with manufacturing and the processing of commodities and other raw materials have complained of falling exports.
A port stoppage earlier in June to protest government taxation policies paralyzed docks exporting corn, soybean, wheat and other agricultural produce.
Fernandez replaced all the key heads of the armed forces in the reshuffle. Brig. Gen. Luis Maria Carena is the new head of the Joint Chiefs of Staff, replacing Jorge Alberto Chevalier.
Division Gen. Cesar Milani takes over from Lt. Gen. Luis Alberto Pozzi as the army chief of staff while Rear Adm. Gaston Fernando Erice replaces Adm. Daniel Alberto Enrique Martin as the navy chief of staff.
Brig. Mayor D. Mario Miguel Callejo takes command of the air force.
The Buenos Aires Herald called the reshuffle a "surprise move."
The changes in the military leadership followed a Cabinet reshuffle in which lawmaker Augstin Rossi was named defense minister, replacing Arturo Puricelli, who was moved to Internal Security.
In published comments Rossi backed the armed forces reshuffle, calling it an "indispensable" move.
He told reporters "the renovation" of Argentine military leadership would allow for younger officers to have opportunities for promotion in the ranks.
"It is the first time in 10 years that we make a shuffle of such characteristics," said Rossi, who is widely regarded as a Fernandez loyalist and headed a "Kirchnerite caucus" in the lower house of Argentine Legislature.
Administration insiders told news media Fernandez had been considering a major shake-up after Argentina's embarrassing experience with the seizure of the naval ship Libertad in Ghana and problems with an ambitious operation to project Argentine sovereignty in Antarctica.
Libertad was seized in Ghana following legal action by an investment company seeking to recover money owed by Argentina since its 2002 debt default.
The vessel sailed home in January after more than two months of an acrimonious detention in the West African country.
Fernandez has also faced congressional scrutiny related to the departure of former Security Minister Nilda Garre and her designation as Argentina's new ambassador at the Organization of American States in Washington. Opposition lawmakers want greater scrutiny of Garre's personal assets.
In January last year Fernandez announced major changes at the top of the military command structure just before she was hospitalized for treatment of thyroid cancer.