Diplomats Hamzeh Doolab Ahmad and Jadidi Sohrab have already left Bosnia and Herzegovina after being declared personae non gratae, the ministry said in a statement.
The Foreign Ministry made a decision to that effect at the proposal of the Security Ministry but the precise reasons for the expulsion have not been explained.
Security Minister Fahrudin Radoncic said earlier the Intelligence and Security Agency (OSA) had registered illicit activities by the two diplomats.
The statement said they diplomats acted contrary to the Vienna Convention on Diplomatic Relations.