"The number of minors already brought back to Germany has reached a high single-digit figure," the foreign ministry source said, adding that the returns were carried out with the consent of the children's parents.
3,000 surrender from Islamic State Syria bastion as end nears
They are now in the custody of their relatives in Germany, the source added.
Among the first young returnees to Germany were three children who arrived with their 31-year-old mother at Stuttgart airport on Thursday, their lawyer Mahmut Erdem said in a statement.
They were taken into custody immediately, the lawyer said.
According to the foreign ministry, at least eight Germans were jailed in Iraq, after they were convicted over their membership of IS.
The foreign ministry said it was aware of cases of German nationals in custody in northern Syria, but added that it did not have direct consular access to them as the embassy in Damascus has been closed.
Nevertheless, the government is looking for ways to repatriate the German nationals, it added.
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With the collapse of the last IS bastion in Syria last month, the fate of foreign fighters and their families has become a significant problem for governments as the conflict against IS draws to a close.
The German interior ministry has said the children are innocent victims, paving the way for their return.
France last month took in five orphans and is dealing with returns on a case-by-case basis.
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