The move comes after recent incidents of armed group activity in the country’s north, near the border with Burkina Faso.
Togo’s President Faure Gnassingbé will oversee the armed forces as part of a reshuffle amid growing security concerns in the northern regions, according to a decree which has been announced.
Under a presidential decree, read by a spokesperson on national television on Friday, the ministry of the armed forces will become part of the presidency.
Until this year, Togo had been spared the frequent violence from armed groups across parts of West Africa over the past 10 years, including in its northern neighbour Burkina Faso.
But a series of attacks, including one in July in which at least 12 people were killed, has forced residents to flee and rattled the armed forces.
In May, eight soldiers were killed and 13 wounded when armed gunmen ambushed an army post in the Kpendjal prefecture near the border with Burkina Faso.
Two months later, the army admitted to killing seven children on July 10 in a blast in the village of Margba, in Tone Prefecture, in its northernmost region Savanna region. In a statement, the military said the youngsters were mistaken for a group of fighters who entered the country on the basis of intelligence gathered.
The minister of the armed forces, Marguerite Gnakadè, has stepped down. The Chief of Staff of the Togolese Armed Forces, Brigadier General Dadja Maganawé, has been replaced by Air Brigadier General Tassounti Djato.