The arrest warrants were issued for 219 soldiers in active service as part of an ongoing investigation into the presence of FETO in the Turkish Army.
The soldiers, including four colonels, are being investigated on suspicions of contacting with the terror group via pay-phone.
Prosecutors also ordered searches and seizures for the suspects.
Police are seeking the suspects to arrest.
FETO and its U.S.-based leader Fetullah Gulen orchestrated the defeated coup of July 15, 2016 which left 251 people martyred and nearly 2,200 injured.
Ankara also accuses FETO of being behind a long-running campaign to overthrow the state through the infiltration of Turkish institutions, particularly the military, police, and judiciary.