The French ambassador to Burkina Faso, Luc Hallade, is "still at work" in the capital Ouagadougou, a French diplomatic source told AFP on Tuesday.
"The team is doing an outstanding job in difficult conditions," the source added, contradicting an announcement on Monday by Burkina Faso's military junta that he had been expelled.
The former French colony has seen a surge in anti-French sentiment as it moves to develop closer ties with Russia.
Government spokesman Jean-Emmanuel Ouedraogo confirmed to the Associated Press that Ambassador Luc Hallade was asked to leave, but provided no further details on Monday.
The announcement of Hallade's expulsion comes less than two weeks after the United Nations’ resident and humanitarian coordinator in Burkina Faso, Barbara Manzi, was also declared persona non grata.
Burkina Faso has been wracked by violence linked to al-Qaida and the Islamic State group that has killed thousands and displaced nearly two million people.
The current military regime overthrew a previous junta last year, claiming it had not done enough to stop the fighting. The previous junta had cited the same reason for seizing power from a civilian government months earlier.
Anti-French sentiment has been growing in the former French colony since the new junta leader, Capt. Ibrahim Traore, seized power in September.
He has been more overtly open to working with other countries, notably Russia. Last month Burkinabe Prime Minister Apollinaire Joachim Kyelem de Tambela visited Russia to strengthen relations and consolidate efforts to combat extremists in the region, according to Russia’s foreign ministry.
France sent troops to West Africa’s Sahel region in 2013 when it helped drive Islamic extremists from power in northern Mali, but is facing growing pushback from local governments that say the French soldiers have yielded few results against the jihadis. French forces left Mali last year after relations with the junta frayed. The French still have several hundred special forces troops based in Burkina Faso.
The announcement of Hallade’s expulsion comes one year after Mali’s junta also ejected France’s ambassador there.
While Burkina Faso's military leaders list restoring security as their chief priority, extremist attacks have continued and are escalating.
Last week at least ten people were killed when a bus hit a roadside bomb in the east. Jihadis have besieged towns, preventing people from moving freely and creating a humanitarian crisis that's pushing tens of thousands to starvation.
Analysts said the announcement of the French envoy's expulsion wasn't a surprise as the junta is following in Mali’s footsteps, and the question is whether Russia will now expand its influence in the region.
“This will clearly sharpen polarisation among (West African countries), between the states that are opposed to the junta's policies and those that want to transition towards democracy,” said Samuel Ramani, associate fellow at the Royal United Services Institute, a UK-based defence and security think tank.