The announcement by the French army follows weeks of tensions between Paris and Niger's new military rulers, who seized power on July 26.
President Emmanuel Macron, who had sought to make a special ally of Niger, announced on September 24 the withdrawal of 1,400 French troops from the country "by the end of the year", complying with a demand by the new regime in Niamey.
Macron said that military cooperation with Niger was "over".
France's ambassador to Niamey last week also returned home from the West African country after the regime demanded his expulsion.
"We will begin our disengagement operation this week, in good order, safely and in coordination with the Nigeriens," the military headquarters said.
The French soldiers are in Niger as part of a wider fight against jihadists across the Sahel region.
Around 1,000 soldiers and airmen are deployed at the French base in Niamey.
Another 400 are deployed alongside local troops in Ouallam and Ayorou in northwestern Niger, near the borders with Burkina Faso and Mali.
The "three borders" zone is known as a haven for the Islamic State group.
The soldiers based at Ouallam will be the first to leave, Niger's military rulers responded in a statement on social media Thursday.
The airbase at the capital Niamey will then be dismantled by the end of the year, they added.
- 'Our interests, conditions' -
Soldiers withdrawing from the area will need cover to leave their exposed forward positions, the military headquarters said.
This possibly could include air support from the larger force at the airbase outside Niamey.
Niger's military rulers said in the statement that they would be "attentive to ensure that this withdrawal takes place with respect for our interests and according to our conditions".
The French troops have been living with uncertainty since the new regime began demanding their departure, with irregular supplies of food and repeated anti-French demonstrations outside the Niamey base.
France had reinforced its presence in Niger after another coup-born military regime in Mali demanded its forces' departure.
Paris had added armoured vehicles and helicopters to the drones and fighter jets that were already deployed.
Its troops will now have to withdraw either via Benin to the south -- at odds with the Niamey regime -- or Chad to the east, the site of France's headquarters for the Sahel theatre.
For now, Niamey forbids French flights over its territory.
- Algerian mediation? -
The coup against Niger's democratically elected president Mohamed Bazoum was the third such putsch in the region in as many years.
It followed similar actions in fellow former French colonies Mali and Burkina Faso in 2021 and 2022 respectively.
Nigeria on Thursday welcomed an Algerian offer to mediate talks with the military regime, which includes a proposed six-month transition period.
Nigeria holds the rotating presidency of ECOWAS, a union of 15 West African countries, which threatened armed intervention after the rebel officers toppled Bazoum.
Nigerian Foreign Minister Yusuf Maitama Tuggar, in an interview with France 24, said that ECOWAS welcomed all parties "seeking for a peaceful resolution to this imbroglio (including) Algeria".
He added that diplomacy was still the favoured path, but that military intervention was "not off the table".
Algeria, which shares a border with Niger, has said it opposes any armed intervention with its neighbour, and has proposed a diplomatic solution.
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