The three were declared "persona non grata" and told to leave the country in 48 hours, the foreign ministry said in a note dated Tuesday that was sent to the French embassy.
Since coming to power in a September 2022 coup, the junta has distanced the West African nation from France, which ruled the country until 1960. It has cancelled a 1961 military accord between the two countries and the French ambassador was withdrawn after the coup.
On December 1, four French officials were arrested, charged and imprisoned in the capital Ouagadougou, according to a French source.
The Burkinabe authorities said they were intelligence agents but the French source said they were IT support staff.
The four are now under house arrest, according to Burkina security sources.
In response Thursday, French foreign ministry spokesman Christophe Lemoine said there were "no legitimate grounds" for Burkina Faso to expel of its diplomats this week.
"There were no legitimate grounds for the Burkinabe authorities' decision. We can only deplore it," he said. Lemoine said allegations against them were "unfounded."
In December 2022, Ouagadougou expelled two French nationals working for a Burkina Faso company for alleged espionage.
France has ended anti-jihadist military missions in Mali and Burkina Faso and more recently began to withdraw forces from Niger—all three countries where juntas are now ruling after coups.
Burkina Faso has increasingly turned to Russia, Mali and Niger for security assistance.
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