He added that military cooperation was “over” and French troops would withdraw in “the months and weeks to come” with a full pullout “by the end of the year”.
France has maintained some 1,500 troops at its base in Niger and refused a request by the new military rulers for its ambassador to leave.
Thousands of people have protested in recent weeks in the capital Niamey, including outside a military base housing French soldiers. The new rulers had been demanding the exit of the French ambassador and troops after Macron refused to recognise the coup.
The development comes as France’s troops have also been asked to leave its former colonies Mali and Burkina Faso.
“This is definitely a small victory for the government in transition, and perhaps an embarrassment for the French who have seen Mali, Burkina Faso and now a third country in the Sahel where it is being asked by the government in place to leave the country,” said Al Jazeera’s Nicolas Haque, reporting from Senegal’s capital Dakar.
“He [the French ambassador] has essentially been held hostage inside the embassy. The Niger security forces wouldn’t let anyone in or out. He has been surviving on the food rations inside the embassy.”
The regional bloc the Economic Community of West African States (ECOWAS) imposed sanctions in the wake of the July coup, and warned that it could intervene militarily if diplomatic efforts to return Bazoum to power fail, as a last resort. But ECOWAS dialed back its rhetoric as regional countries threw their weight behind the new military rulers.
The three Sahel countries – Niger, Mali and Burkina Faso, which have all witnessed coups in recent years – formed a mutual defence pact on September 16 against possible threats of armed rebellion or external aggression.
With tensions mounting, Macron said he told the ousted Bazoum on Sunday that “France has decided to bring back its ambassador, and in the coming hours our ambassador and several diplomats will return to France.”
Macron reaffirmed France’s position that Bazoum was being held “hostage” and remained the “sole legitimate authority” in the country.
“He was targeted by this coup d’etat because he was carrying out courageous reforms and because there was a largely ethnic settling of scores and a lot of political cowardice,” he said.
Macron noted that France’s military presence in Niger was in response to a request from Niger’s government at the time.
Niger’s military rulers ended military cooperation with France following the coup after claiming that Bazoum’s government was not doing enough to protect the country from the armed rebellion in the country’s west, which is part of the semi-arid Sahel region.
In the last decade, the Sahel region that stretches to central Mali, northern Burkina Faso and western Niger has become the epicentre of violence by armed groups linked to al-Qaeda and ISIL (ISIS).
Western countries had partnered with Bazoum to tackle the growing influence of armed groups, and poured millions of dollars of military aid and assistance to shore up Niger’s forces.
Meanwhile on Friday, the military government accused United Nations Secretary-General Antonio Guterres of “obstructing” the West African nation’s full participation at the UN’s annual meeting of world leaders in order to appease France and its allies.