The number was released by the Gulf state's Ministry of Administrative Development, Labour and Social Affairs as Qatar announced it had abolished its controversial "kafala" labour system from today.
All the flights were paid for by the state, said officials, who gave no more details about the nature of the abuses or any measures taken against employers.
There are 2.1 million migrant labourers in Qatar, according to the ministry, from countries including Nepal, Bangladesh and India.
Many are working on World Cup infrastructure projects.
Doha has introduced a new contract-based system for foreign workers from December 13, which it says will give more protection to workers and safeguard their rights.
Under "kafala", all foreign workers working in Qatar required a local sponsor, in the form of an individual or company, and needed their permission to switch jobs or leave the country.
Under the new system, workers will still need the permission of their employer to leave the country.
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