The troops stopped the smugglers Thursday morning near the village of Kusakli in the Reyhanli district of Hatay province, Today's Zaman reported.
It was unclear whether the smugglers were on the Syrian or Turkish side of the border.
After stopping the smugglers, the troops then came under rifle fire from the village, the Turkish military said in a statement.
The smugglers, which included up to 1,000 people on foot, 150 on horses and 40 vehicles, fled the scene, leaving behind 35 diesel drums.
In a separate incident on Wednesday, a soldier was injured when a group of 10 smugglers set a diesel drums on fire. The soldier was severely injured and was hospitalized in Ankara.