The agent was charged Sept. 23 and has been placed on administrative leave, nearly three years after he fatally shot 16-year-old José Antonio Elena Rodríguez.
There had been another shooting near the same housing complex just hours earlier.
The Mexican government said Thursday that it "welcomed" the decision to indict the agent.
Firefighter Matthew Sánchez had already sent paramedics to the scene of the June 26 shooting at a house during the call when he and the caller got into an argument, fire and police officials said.