"We have decided to recall our ambassador in Paris, to conduct consultations on the state and perspectives of our bilateral cooperation", the ministry said in a statement.
Protests by opponents of the French military presence have surged in Burkina, partly linked to perceptions that France has not done enough to tackle an Islamist insurgency that has spread in recent years from neighbouring Mali.
France on Wednesday said it would withdraw its troops in the next month after the military junta asked it to leave.
(Reporting by John Irish, writing by Tassilo Hummel, editing by Alex Richardson)
