The CIA operatives and a member of the Mexican navy were in a sport utility vehicle with diplomatic plates when the officers riddled the SUV with 152 bullets, the Los Angeles Times reported.
The police officers' actions were deliberate, prosecutors said in a statement. In a phone interview, however, a spokesman for the prosecutor's office said the attack could have been the result of "confusion."
Prosecutors allege the officers acted deceptively during the investigation. The officers were in plain clothes and driving civilian cars when they attacked the Americans, but were in uniform and driving squad cars when they appeared before investigators.
The U.S. embassy in Mexico City and federal police worked in "close collaboration" in developing the case, Mexican officials said.