The accident happened in a tank that was undergoing maintenance and cleaning, a spokeswoman for the company said in a statement. No details were provided.
A spokeswoman for city prosecutors says the accident occurred early Sunday and that investigators are looking into whether the workers died from inhaling toxic fumes. The official spoke on condition of anonymity because she was not authorized to discuss the case, according to the Associated Press.
Plant manager Francisco Lopez Bravo told local media the workers were trapped inside the cistern while doing maintenance work.
Grupo Modelo said it has informed authorities and has begun investigating the accident.
"Modelo is deeply sorry for this incident and will support the affected families permanently," the statement said.
The spokeswoman did not say whether the accident would affect production.
Modelo's Mexico City plant was the company's first and it began operating in 1925, according to the company's website.
The plant had a capacity of 11.1 million hectoliters in 2011, about 16 percent of Modelo's total.
Modelo and ABI on Friday said they had reached an agreement for a framework to settle a lawsuit brought by the U.S. Justice Department in January over concerns the deal would lead to higher beer prices in the United States.