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France will repatriate its ambassador in Niger in the “coming hours” and withdraw the 1,500 soldiers it has based there by the end of the year as it moves to end a diplomatic stand-off with the junta that seized power in the west African country in July.

President Emmanuel Macron said in an interview on France 2 television on Sunday night that he had informed the deposed president Mohamed Bazoum, who remains under house arrest, of the decisions.

“Our ambassador and several diplomats will return to France,” Macron said.

“We will also end our military co-operation with the authorities effectively in power since they no longer want to fight against terrorism,” he said, adding that France would negotiate with local authorities to ensure a “calm and orderly” troop withdrawal.

There was no immediate reaction to Macron’s announcement from the ruling National Council for the Safeguard of the Homeland (CNSP) junta in Niger.

For much of the past decade, France has stationed thousands of troops in the Sahel region south of the Sahara desert at the request of African leaders to fight jihadist groups.

But a wave of coups in Mali, Burkina Faso and, most recently, Niger has led to the exit of French troops who have been ordered to depart by coup leaders in the former French colonies.

French special forces left Burkina Faso in February at the request of the military junta there and Niger’s military leaders immediately terminated the co-operation agreement with France in the aftermath of the coup.

The French withdrawal from Niger, which under Bazoum had been a regional ally, will be a blow to western efforts to fight al-Qaeda and Isis affiliates in the region. The US military also has a significant military presence in Niger, including a base used for drone operations.

Like the US and EU, France has not recognised the military-led government in Niger and still sees Bazoum as the only legitimate democratic leader. For months, Paris has refused to recall its ambassador or to bring back its troops despite pressure from the new Niger government to do so.

Tensions between France and Niger have risen recently with Macron saying that France’s ambassador Sylvain Itté had been “taken hostage” in the embassy, referring to how he and his team were holed up and surviving on military rations.

The CNSP had given Itté 48 hours to depart in late August, and Niger’s top court approved his expulsion and revoked his diplomatic immunity.

Several protests demanding the withdrawal of French troops have taken place outside a military base in the capital Niamey where French forces are stationed.

Macron defended France’s military record in the Sahel and argued that the security situation had worsened since the coups.

“We will continue to accompany African countries in the fight against terrorism, but only if it is at the request of democratically elected governments or regional bodies,” he said. “I am very worried about the region.”