Officials confirmed Rafael Caro Quintero is still under indictment for the crime in Los Angeles.
Caro Quintero was released from prison Friday after serving 28 years of a 40-year sentence for the death of Drug Enforcement Agent Administration agent Enrique Camarena.
The suspect was indicted in 1987 in Los Angeles but released this week after a Mexican federal court ruled he had been improperly tried in a federal court for state crimes.
"The Department of Justice, and especially the Drug Enforcement Administration, is extremely disappointed with this result," it said in a statement.
The Association of Former Federal Narcotics Agents blamed corruption within Mexico's justice system for his early release.
The DEA, meanwhile, said it will continue its efforts to ensure Caro Quintero faces charges in the United States.
Caro Quintero was a founding member of one of Mexico's earliest and biggest drug cartels. He helped establish a powerful cartel based in the northwestern Mexican state of Sinaloa that later split into some of Mexico's largest cartels, including the Sinaloa and Juarez cartels.
But he wasn't tried for drug trafficking, a federal crime in Mexico. Instead, Mexican federal prosecutors, under intense pressure from the United States, hastily put together a case against him for Camarena's kidnapping and killing, both state crimes.
The Associated Press contributed to this report.