The official, confirming a report by the Dogan news agency, said two other men were also arrested, without giving details.
The Belgian, Ahmet Dahmani, was arrested at a luxury hotel in the southern coastal city of Antalya. Dogan said the 26-year-old had been staying in a five-star hotel in the popular tourist destination since Nov. 16.
Dogan said the two other men, both Syrian citizens, were detained on a nearby highway on suspicion they had been sent by Islamic State in Syria to ensure Dahmanis safe passage across the border and were planning to meet him.
Dogan, citing court sources as Reuters reported, identified the two men as 29-year-old Ahmet Tahir and 23-year-old Muhammed Verdi.
Counter-terrorism police first became aware of Dahmani when he arrived on a flight to Antalya and tracked him to the hotel in the Manavgat district of the city, Dogan said.
Separately, Turkey deported a group of Moroccans detained at Istanbuls main airport this week over suspected links to Islamic State.
The eight, who said they had arrived at Ataturk airport on Tuesday night from Casablanca for a holiday, were detained by border police and questioned by profiling experts who flagged them as suspected militants, a government official said.