The development comes a day after Paris announced it would withdraw its troops from the African country.
France has said that it was recalling its ambassador from Burkina Faso, a day after agreeing to demands from the African country's demand to pull out troops from the former French colony in the Sahel region.
"In the context of the latest developments in Burkina Faso, we have decided to recall our ambassador to Paris for consultations on the state and perspectives of our bilateral relations," the foreign ministry said on Thursday.
The development comes a day after Burkina Faso on Monday requested France to withdraw its military, which was deployed to help local forces battle insurgents linked to the al Qaeda and Daesh terrorist organisations.
The West African country said it has decided to end a military pact that allowed the presence of French troops because it is in line with the transition government’s vision for the Burkinabe people to defend their country.
READ MORE: "Burkina Faso demands French troop withdrawal 'within a month'"
It noted, however, that the request does not mean the end of diplomatic ties between the two countries.
A French diplomatic source revealed that the request regarding the agreement of 2018 on the status of the French forces in the country will take effect next month, French radio broadcaster Europe 1 reported.
"We will respect the terms of the agreement and proceed with the request," the source said.
Relations between France and Burkina Faso have been low since soldiers seized control of the African country in September last year.
Several demonstrations have been reported against the French military presence in the country on perceptions that it has been ineffective against the terrorism that has been raging in the country since 2015.
France maintains 400 special forces based in the country.