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The Istanbul governor's office said that 42,888 "illegal" migrants had been arrested and sent to repatriation centers for their expulsion from Turkey. The announcement did not disclose their nationality.
But it is reported that 6,416 Syrians were placed in "temporary shelter centers".
The campaign by the Turkish authorities aimed to reduce the number of unregistered refugees in Istanbul, which is known as Turkey's largest economic center and city.
There are about 3.6 million Syrian refugees in Turkey, though technically they are only under "temporary protection" because the government does not offer them official refugee status.
According to the rules, they must stay in the province to which they are assigned, and can only visit other cities on short terms, AFP reports.
Officials said in July that 547,000 Syrians had been officially registered in Istanbul.
Turkey's Interior Minister Suleyman Soylu said Turkish authorities aimed to deport about 80,000 undocumented migrants by the end of the year.
Turkey has faced minor social problems despite the influx of refugees from its eight-year conflict with its southern neighbor.
But the economic downturn that the country suffered has raised tensions, and analysts say the refugee issue is likely to have contributed to the ruling party's surprise defeat in local elections this year.
Human Rights Watch and Amnesty International are among several groups accusing Turkey of repatriating Syrian refugees against their will - which the government has denied.
Turkey has become a "dam", preventing migrants from crossing the Western Balkans and from there to Europe.
However, several thousand of them have reached Europe.
The European Union has funded Turkey with hundreds of millions of dollars in order to keep refugees on its territory.