A contingent of 120 soldiers left for France from a military airport in the capital, the ministry said in a statement on Facebook, 10 days after French fighter aircraft left the Sahel country for good.
Chad had been a key link in France's military presence in Africa and its last foothold in the wider Sahel region after the forced withdrawal of French troops from Mali, Burkina Faso and Niger in the wake of a series of military coups.
But it announced on November 28 its decision to end a longstanding defence accord with Paris.
"At midday, 120 French soldiers took off from the military airport of N'Djamena on board an Airbus A330 Phoenix MRTT, headed for France," the ministry said in a statement on Facebook.
The French army, which had some 1,000 personnel in the country, did not immediately comment on the announcement.
The departure on Friday of French soldiers took place in the presence of Chadian military authorities, which "testifies to the intensity of cooperation between the two countries in the field of security", the statement said.
- Shifting alliances -
French soldiers and fighter aircraft have been stationed in Chad almost continuously since the country's independence in 1960, helping to train the Chadian military.
The planes provided air support that proved crucial on several occasions in stopping rebels moving to seize power.
Chad's decision to break military ties with France came only hours after a visit by French Foreign Minister Jean-Noel Barrot, whose delegation appeared not to have seen it coming.
The central African country was the last Sahel nation to host French troops.
Its decision also came shortly after Senegal's President Bassirou Diomaye Faye told AFP in an interview that France should close its military bases there.
Military equipment will leave Chad on an Antonov 124 plane planned for the coming days, the Chadian ministry statement said.
Military vehicles from three French bases are also due to be repatriated to France via the Cameroonian port of Douala, it added.
The military authorities in Mali, Burkina Faso and Niger have pivoted towards Russia in recent years.
Chad's leader General Mahamat Idriss Deby Itno has also sought closer ties with Moscow in recent months, but talks to strengthen economic cooperation have yet to bear concrete results.
Deby described the agreement as "completely obsolete" and no longer aligned with the "political and geostrategic realities of our time".
Chad would not follow a "a logic of substitution of one power for another, much less... an approach of change of master".
The Chadian president has previously said that the ending of the defence agreement did not mean "a rejection of international cooperation or a questioning of our diplomatic relations with France, whatsoever".
Paris has been preparing for years what it called a "reorganisation" of military relations after the forced departure of its troops from the western African countries.
In a speech from the French military base in Djibouti on Friday, President Emmanuel Macron said the envisaged an expanded role for the mission there.
The election of Deby in May brought an end to a three-year political transition triggered by his father's death in clashes with rebels in 2021.
Longtime ruler Idriss Deby Itno had received support from the French army to quell rebel offensives in 2008 and 2019.
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