The ministry said in a statement it had summoned French ambassador Anne Boillon to express a "strong protest over the actions of two employees of the French Embassy."
Without providing further details, it said the two had been declared personae non gratae and ordered to leave the country within 48 hours.
The move came amid tense relations between the countries as Baku has accused France of being biased towards Armenia during European-mediated peace talks with its arch-foe.
In November, Azerbaijani President Ilham Aliyev accused France of inciting conflicts in the Caucasus by arming Armenia.
Azerbaijan and Armenia have fought two wars over the disputed Nagorno-Karabakh region.
Baku reclaimed the enclave in September after a lightning offensive against Armenian separatists who had controlled it for three decades.
Armenia and Azerbaijan had said a comprehensive peace agreement could be signed by the end of the year, but internationally mediated negotiations between the ex-Soviet republics have made little progress.
Aliyev and Armenian Prime Minister Nikol Pashinyan have met on several occasions for talks under the mediation of the European Union.
But in October, Aliyev refused to attend negotiations with Pashinyan in Spain, over what he said was France's "biased position".
French President Emmanuel Macron and German Chancellor Olaf Scholz had been set to mediate the talks along with European Council President Charles Michel.
Home to a large Armenian diaspora, France has been routinely accused by Azerbaijan of pro-Armenian bias over the Caucasus countries' territorial conflict.