Turkish profiling teams have also interviewed 9,500 people upon their arrival in Turkey, Ibrahim Kalin, a spokesman for President Recep Tayyip Erdogan, told reporters.
Some 2,000 of them were denied entry as a result.
Around 2,770 suspects, including 1,232 foreigners, have been caught in police sweeps and 954 of them are being prosecuted, Kalin said.
He didn't give further details. Turkish officials have refused to provide a breakdown of the jihadi suspects by nationality or give details on the countries they have been deported back to.
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The agency said 492 of the militants were killed in air raids while another 370 were killed by artillery fire. The agency didn't specify how the figures were obtained and it wasn't possible to verify them independently.
Turkey, long accused of turning a blind eye to the extremists crossing into Syria, has now taken a larger role in the fight against IS, opening a key air base in southern Turkey to the US-led coalition fighting the extremists and reinforcing its border to prevent infiltrations.