France's ambassador in Niger was flown out of the country early on Wednesday morning, Reuters news agency reports quoting two security sources,
It comes around one month after the military government ordered his expulsion.
The junta that seized power in a July coup ordered French ambassador Sylvain Itte to leave the country within 48 hours at the end of August in response to what they called actions by France "contrary to the interests of Niger".
But the order was at first ignored by France, who has refused to recognise the coup leaders, triggering daily protests in front of the French embassy.
French President Emmanuel Macron said this month that Itte and his staff were effectively being held hostage at the embassy.
Over the weekend, Macron said the ambassador was being pulled out and would return to France. He also announced the withdrawal of 1,500 French troops.