Cumhuriyet newspaper's editor-in-chief Can Dundar, and the paper's Ankara representative, Erdem Gul, were sent to a prison in Istanbul late yesterday, accused of willingly aiding a terror organisation and revealing state secrets.
The incident comes amid deepening concerns over media freedoms in Turkey, which aspires to join the European Union.
In May, the paper published what it said were images of Turkish trucks carrying ammunition to Syrian militants.
The government had initially denied the trucks were carrying arms, maintaining that the cargo consisted of humanitarian aid. However, some officials later suggested that the trucks were in fact carrying arms or ammunition destined to Turkmen in Syria.
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Prosecutors launched an investigation into the journalists after President Recep Tayyip Erdogan filed a criminal complaint.
Crowds filled the yard and a street outside of Cumhuriyet's headquarters, chanting: "Free press cannot be silenced."
At a separate protest in Ankara, police used tear gas to break up a gathering of journalists hoping to march to Cumhuriyet's office in the city.
The US Embassy expressed concern over Dundar and Erdem's arrests and at the apparent pressure being exerted on Cumhuriyet.
"We hope the Turkish courts and authorities will uphold the fundamental principle of media freedom enshrined in the Turkish Constitution," the Embassy said on Twitter.