The Russian-made MiG-21 crashed around 2:00 pm (1300 GMT) in an uninhabited forested area near the eastern town of Slatina, the ministry said in a statement.
The two pilots were found in a stable condition and will be taken to a hospital for a check-up, it said.
The ministry did not elaborate on the cause of the crash.
NATO and EU member Croatia last year bought a batch of used Rafale planes from France to replace its obsolete MiGs.
The first of the 12 Rafale planes are expected in Croatia by 2024.
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