The 17 have been charged with membership of a terrorist organisation and working on behalf of the "parallel state", common official shorthand for President Recep Tayyip Erdogan's arch enemy the US-based preacher Fethullah Gulen.
A total of 32 soldiers detained after prosecutors issues warrants at the weekend had appeared before the Istanbul court but 15 were allowed to go free, 10 of them under judicial supervision.
A date for the trial has yet to be set.
A series of documents were then leaked on the Internet indicating that the seized trucks were actually National Intelligence Agency (MIT) vehicles delivering weapons to Syrian Islamist rebels fighting President Bashar al-Assad.
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Turkey has vehemently denied aiding Islamist rebels in Syria, such as the Islamic State (IS) jihadist group, although it wants to see Assad toppled.
Turkey earlier this year imposed an all-out media blackout, including on Facebook and Twitter, prohibiting publication of the allegations.
As well as membership of a terror group and working for the parallel state, they have been charged with illegal eavesdropping, forging illegal documents and working to overthrow the government.
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.
The Turkish authorities have sought to blame the scandal on Gulen who Erdogan accuses of running a parallel state through supporters in the judiciary and security forces with the aim of usurping him.
Supporters of Gulen, who have been pressured by a wave of arrests in the past months, ridicule the allegations and accuse Erdogan of leading Turkey to dictatorship.