Arrest warrants were issued for 10 soldiers, of whom eight had been detained by Friday night, the official Anatolia news agency reported.
They have been accused of membership of a terrorist group, impeding the work of the government and espionage, it said. They should now appear in court to decide whether to remand them in custody ahead of trial.
The arrests are the latest in a string of detentions related to the stopping and searching of trucks in the southern provinces of Hatay and Adana near the Syrian border in January 2014 on suspicion of smuggling arms into Syria.
Turkey has vehemently denied aiding Islamist rebels in Syria, such as the Islamic State (IS) group, although it wants to see Assad toppled.
More From This Section
The government has imposed a full-blown media blackout, including on social networks, and the investigation is being carried out in the utmost secrecy.
Earlier this month, Turkey arrested the four prosecutors who had ordered the search of the trucks and they are now in prison ahead of trial.
Another 19 soldiers were also placed under arrest pending trial in April, Anatolia said.
Not including the latest arrests, Anatolia said that a total of 47 people were being held in the investigation.
The Turkish authorities have sought to link the affair to US-based preacher Fethullah Gulen who President Recep Tayyip Erdogan accuses of running a parallel state through supporters in the judiciary and police with the aim of usurping him.
Supporters of Gulen, who have been pressured by a wave of arrests in the past months, reject the allegations.
The controversy erupted on January 19, 2014 when Turkish forces stopped trucks bound for Syria suspected to have been loaded with weapons. But they then found MIT personnel were on board.