It ordered the arrest of RSF representative Erol Onderoglu, journalist Ahmet Nesin and academic Sebnem Korur Fincanci.
RSF said it was "an unbelievable low for press freedom in Turkey".
The arrests come despite the EU pressuring Ankara to stop prosecuting academics and journalists.
The three had reportedly participated in a solidarity campaign in support of Ozgur Gundem, a pro-Kurdish newspaper.
Turkish media say they each acted as chief editor for a day.