Guinea junta leader Colonel Mamady Doumbouya had sacked 42 army officers among them military top brass.
They include chief of the general staff of the armed forces general Namory Traoré, and the head of the gendarmerie (military police), Ibrahima Baldé, and former military president General Sekouba Konate, who were forced to retire.
The heads of all the wings in the armed forces were also retired and replaced with low-ranking officers.
The announcement was made on Tuesday via a statement from the presidency, invoking presidential decrees.
In a separate statement, Col Doumbouya appointed 28 of the retired generals to the High Council of National Defence, the body in charge of national security matters.
The changes in the army come two weeks after Col Doumbouya, who led a coup against President Alpha Conde on September 5, was sworn in as transition president.
Last week he appointed a new prime minister to head the process of transitioning the country to civilian rule.
Political analysts see the move to retire the generals as an attempt by Doumbouya to assert control over the army, which is thought to be loyal to Conde. Most of the military top brass who were retired are known allies of the former president.
Among those appointed to the High National Defence Council is General Konate, who had earlier endorsed the coup.
Konate served as the interim president of Guinea from December 2009 to December 2010. Prior to that, he was the second in command of the National Council for Democracy and Development junta, which had seized power in 2008 following the death of President Lansana Konteh.
He replaced the then coup leader, Mousa Dadis Camara, who had been shot on the head and flown out of the country for medical treatment in a failed assassination bid.
Konate subsequently presided over Guinea’s first democratic elections in 2010, through which Conde came to power. He was appointed to head the AU’s military forces shortly after handing over power to Conde.
The new top four heads of the armed forces are Colonel Sadiba Coulibaly, Chief of the General Staff of the Armed Forces; Colonel Ahmed Mohamed Oury Diallo, Deputy Chief of the General Staff of the Armed Forces; Colonel Balla Koïvogui, Chief of Staff of the Army; and Colonel Ibrahima Sory Bangoura, Deputy Chief of Staff of the Army.