The 19-member group consists of three families with children and a single.
They have all said that they intend to apply for international protection in Croatia, the ministry said.
The Afghan nationals had all been vetted prior to their employment with the EU Delegation.
The European External Action Service (EEAS) has called on EU members to take in EU staff from Afghanistan, around 500 Afghan nationals, mostly interpreters, logistics staff and their families.
Croatia has responded to the appeal, deciding to accept 20 persons whose lives and security are threatened by the restoration of the Taliban regime.
The ministry’s immigration service is now in charge of the Afghan nationals.
Since the group includes as many as ten minors, it will be accommodated at a ministry facility for vulnerable groups.
The ministry said that it would not provide further information on the immigrants for the sake of their security.
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