Mexican soldiers opened fire on a group of 33 migrants, killing six, said the defense ministry in a statement on Wednesday.
The migrants were in a truck which tried to evade a military patrol on Tuesday night.
The ministry said it reaffirmed "its commitment to act in strict accordance with the rule of law, under a policy of zero-impunity, and is ready to help the civil authorities to shed light on the facts."
Ten others were injured in the incident. The ministry said the migrants hailed from Egypt, Nepal, Cuba, India and Pakistan.
The nationalities of the deceased were not clear, but the ministry said it would contact the corresponding embassies.
The UN Refugee Agency in Mexico expressed concern over the event, adding that "people in migration are exposed to great risks during their journey, and that is why it is indispensable they have legal means of access, travel, and integration to avoid tragedies like these."
Why did the soldiers open fire?
The incident happened near the town of Huixtla in southern state of Chiapas, close to the Guatemalan border. It is a common route for migrants, who are often smuggled in densely packed vehicles.
Two vehicles similar to those used by criminal groups in the area were following the truck.
Mexican soldiers said they heard explosions, due to which they opened fire.
Four were killed at the scene, and two others died after being brought to a nearby hospital. Local prosecutors confirmed they had died of gunshot.
The defense ministry said the two soldiers who opened fired have been removed from their posts. They could face prosecution as well as a military trial.
In 2021, Mexico's National Guard had also opened fire on a truck of migrants in the same area, killing one.
Mexico facing US pressure to curb migration
Mexico is facing much pressure from the United States of America to reduce the number of migrants arriving at their shared border.
A vast number of migrants try to enter the US from Mexico to escape economic hardship and violence. In recent months, the number of migrants arriving in the US has dropped as the country prepares for elections.