“We believe that two of the dead came from Germany, that means that they had their permanent addresses here,” a Foreign Ministry spokesperson said on Monday.
One of the deceased in the New Year shooting had dual German and Turkish nationality.
“Our current understanding is that the other man only had Turkish nationality,” the spokesperson said.
Both men lived in Bavaria.
The spokesperson also added that the three Germans who were injured are being treated in hospital but are not in a life threatening situation.
A total of 39 people were killed in the assault claimed by Isis at the exclusive Reina club on the shores of the Bosphorus and 65 were injured, officials said.
According to Turkish press reports, 11 Turks were killed in the attack alongside 27 foreigners. One victim is still unidentified.