Police arrested the man, identified as Ali al-Aggal and code named Azzov, believed to be the IS group's organiser of Turkey attacks, in an operation in the Turkish capital Ankara, Haber-Turk newspaper reported.
In a separate raid, police held 24 other IS suspects from Iraq and Syria in the Kucukcekmece district of Istanbul, the newspaper said.
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The remaining 15 suspects were planning to cross the Turkish border into conflict zones, the newspaper said.
Police found out that suspected IS jihadists used the building in Kucukcekmece as a "sleeper cell" and seized many documents and digital materials allegedly belonging to the extremist group, according to the report.
Turkey has suffered a series of attacks blamed on IS jihadists including a suicide bombing at a Kurdish wedding in a city close to the Syrian border in August.
The latest arrests come as several embassies, including Britain's, closed Friday for security reasons.
A member of the anti-IS coalition led by the United States, Turkey has started to take an active role in the fight against the jihadist group after it had long been criticised by its Western allies for not doing enough.
Turkey in recent months has also cracked down on the group's sleeper cells and launched an ambitious operation inside Syria to oust jihadists and Syrian Kurdish militia from its frontier.
President Recep Tayyip Erdogan has indicated that Turkey and the United States have discussed an operation to push IS jihadists out of their de facto capital of Raqqah in Syria but there have been no further details.
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