The soldiers have been mobilizing since Tuesday in the departments of San Marcos and Huehuetenango -- mountainous zones inhabited mainly by Indigenous Mayans.
Many residents of these underserved areas survive from growing marijuana and the poppy plants from which heroin and opium are obtained.
Just across the border, the Chiapas state in southern Mexico is in the grips of a war between the Sinaloa and Jalisco New Generation cartels.
The violence has led to food shortages and electricity and internet blackouts as businesses are forced to close and residents cross to Guatemala to shop.
Army spokesman Colonel Ruben Tellez told reporters the objective of the army deployment was to "prevent any possibility of groups with links to transnational organized crime from crossing into Guatemalan territory and causing distress to local populations."
It would also aim to "strengthen governability and security" in the border region.
The two countries share about a thousand kilometers of border with few controls and many illegal crossings by drug traffickers and undocumented migrants.
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