Last week, Erdoğan said Turkey had captured 13 people from Baghdadi's close circle, adding that they were being interrogated. He previously said about 1,200 foreign IS fighters were in Turkish prisons and 287 members, including women and children, were re-captured during Turkey's military offensive into northeast Syria last month.
It was not clear if all those being deported this week were captured in Syria, or in Turkish territory.
Europeans comprise a fifth of the around 10,000 ISIL members held captive in Syria.
According to the German Interior Ministry, more than 80 German IS members are imprisoned in Syria and Iraq.
Relatives of suspected IS militants were also being held at a number of camps for displaced people - the largest of which, al-Hol, housed nearly 70,000 people.
The Turkish offensive prompted widespread concern over the fate of the prisoners, with Turkey's Western allies and the SDF warning it could hinder the fight against ISIS and aid its resurgence.
How will the repatriations work?
It remains unclear whether Turkey will be able to repatriate those who have lost their citizenship.
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"There is no need to try to escape from it, we will send them back to you. The news is not published, or released much later", the source said.
Britain alone has stripped more than 100 people of their citizenship for allegedly joining militant groups overseas. Denmark, Germany and Britain have so far revoked some citizenships.
Last week, Turkey's interior minister said the suspected militants would be sent home, even in cases where governments had stripped suspects of their citizenship.
There was no dispute about these people's German citizenship, he said, and therefore no doubt about them being let back into the country - Germany can't and doesn't refuse entry to its own citizens.
BBC security correspondent Frank Gardner says European intelligence agencies have warned that many of those who survived the final days of IS's last stand will remain highly unsafe radicals, brutalised by the atrocities they have witnessed, and in some cases, committed. European states have largely refused to bring their citizens home for trial, instead they are seeking to transfer them across the border to Iraq, where more than 17,000 men and women have already been charged with terrorism offenses.
He had also said that Turkey is not "a hotel" for ISIL terrorists.
Governments may then find themselves accused of allowing back in risky men and women who pose a risk to national security.