The two men were shot dead on Saturday, days ahead of the triple suicide bombings at Istanbul's Ataturk airport on Tuesday that left 42 people dead, the Anadolu and Dogan agencies said.
One of the suspects, named as Mohammad Arab, was planning an attack either in the Turkish capital Ankara or in the southern city of Adana, Dogan added.
Ankara was the scene of Turkey's worst ever attack last October when 103 people were killed in suicide bombings blamed on IS.
The government has said Islamic State jihadists were likely behind the carnage at Istanbul airport, one of the busiest hubs in Europe.
Turkey has cracked down on IS after a string of deadly attacks blamed on the jihadists, who have seized swathes of land in Iraq and Syria, right up to the Turkish border.
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