The state security agency and state prosecutor's office said in a joint statement Friday that six state agents looking for drug dealers were involved in the incident late Wednesday.
Authorities also said the victim originally reported as a migrant from El Salvador was from Honduras.
On Thursday, state authorities had said migrants verbally assailed the agents and then the officers fired when one migrant pulled a pistol. But there was no mention of the pistol in Friday's statement.
The Casa del Migrante shelter in Saltillo has said a group of migrants left the shelter to board a passing freight train when they were attacked by agents.