The presidential decrees, announced late Thursday, specify no reasons for the reshuffle, but the changes come as the small West African country faces a growing threat from jihadist groups.
"Marguerite Essossimna Gnakade is relieved of her duties as armed forces minister," the first presidential decree stated, saying she has been "called to other duties."
Since November 2021, Togo has suffered at least five attacks, including two deadly ones in the far north of the country, which is plagued by jihadist incursions from across the border in Burkina Faso.
No replacement will be named as the armed forces will be answerable directly to the presidency, under the orders of Gnassingbe, as was the case from 2007 to 2020, another decree stated.
Colonel Tassounti Djato, former chief of staff of the Air Force is promoted to general and "appointed chief of general staff of the Togolese Armed Forces", replacing General Dadja Maganawe, who had occupied the job since late 2020.
West African nations Mali, Burkina Faso and Niger are plagued by jihadist insurgencies, and neighbouring coastal states such as Benin, Ghana, Togo and Ivory Coast have long been concerned about the violence spilling into their territories.
In mid-July, "unidentified armed individuals" carried out a bloody attack in Togo, according to the army, which reported "several dead and a few wounded".
Local media reported that between 15 and 20 civilians were killed.
Last month, local media reported a deadly attack on armed forces in the far north, which AFP was unable to confirm. The authorities refused to comment on the matter.