The country's foreign and defence ministries said in a joint statement that two Airbus A400Ms had flown to Israel for the operation to bring home "families with children and other vulnerable people".
The ministries' statement stressed this had been a diplomatic operation carried out in close cooperation with the Israeli authorities, as any military operation would have required the approval of Germany's parliament.
Germany's foreign ministry has already organised the evacuation of 345 people on two chartered flights via Amman. Another such flight is due to leave the Jordanian capital on Saturday.
Germany is among several countries to organise evacuations for their citizens by land, sea and air from both Iran and Israel, as the two continue to bombard each other.
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