French Foreign Minister Catherine Colonna met Sylvain Itte "to thank him and his teams for his work in the service of our country under difficult conditions," the ministry said in a written statement to AFP.
The return of the ambassador comes two months after a coup in Niger ousted its pro-Paris president and prompted a souring in relations between France and its former colony, with Niger's new rulers demanding his departure.
Itte left Niamey with six colleagues "around 4:00 am" (0300 GMT), a diplomatic source had earlier told AFP.
On Sunday, French President Emmanuel Macron had announced in a TV interview that the ambassador would leave "in the coming hours".
Niger's military leaders -- who overthrew the democratically elected president Mohamed Bazoum on July 26 -- welcomed the announcement.
Born in the Malian capital Bamako in 1959, Itte had been in the post as ambassador to Niger for a year.
His diplomatic career spans 35 years and he was previously ambassador to Uruguay and Angola.
- 'Return to constitutional order' -
The Junta had told Itte to leave the country after they overthrew Bazoum and took away the envoy's diplomatic immunity and visa.
But a 48-hour ultimatum for him to go, issued in August, passed with him still in place, as the French government refused to comply or to recognise the military regime as legitimate.
Paris had said that only Bazoum's deposed government could order the envoy out.
Macron's office reiterated France's support for the ousted president on Wednesday.
He had told Hassoumi Massaoudou, foreign minister in the overthrown government, that France would continue to work "for a return to the constitutional order in Niger", the Elysee Palace said.
Macron also announced in his Sunday TV interview that French troops would withdraw from Niger in "the months and weeks to come" with a full pullout "by the end of the year" -- another demand of the Niger regime.
The French president, who had sought to make a special ally of Niger, said military cooperation was "over".
France keeps about 1,500 soldiers in its former West African colony as part of an anti-jihadist deployment in the Sahel.
The coup against Bazoum was the third such putsch in the region in as many years, following similar actions in fellow former French colonies Mali and Burkina Faso in 2021 and 2022, respectively.
The earlier coups also forced the pullouts of French troops.
- Ousted leader 'held hostage' -
Macron said on Sunday that Niger's post-coup authorities "no longer wanted to fight against terrorism".
He also reaffirmed France's position that Bazoum was being held "hostage" and remained the "sole legitimate authority" in the country.
The elected president has remained confined in the presidential palace with his wife and son.
The junta had welcomed Macron's announcement on Sunday as "a new step towards sovereignty" but has said the timeframe for the military pullout "must be set out in a negotiated framework and by mutual agreement".
Niger, like Burkina Faso and Mali, has been targeted by jihadist attacks for several years.
In recent weeks, tens of thousands of people have joined demonstrations and gatherings in Niamey calling for the withdrawal of the French troops from the country.
The United States, which has some 1,100 military personnel in Niger, has said it will "evaluate" its future steps on the crisis following France's announcement.
US Defense Secretary Lloyd Austin, during a trip to Angola on Wednesday, said Washington will continue to support "civilian-led" militaries in Africa.
"When generals overturn the will of the people and put their own ambitions above the rule of law, security suffers," he said, decrying "autocrats" who "undermine free and fair elections".
The US Defense Secretary did not name any country, but his comments appeared to be a clear reference to Niger.
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