The shootings Tuesday about five miles north of the border near Bisbee left one agent dead and another wounded.
Agent Nicholas Ivie and two others had responded to an alarm triggered by a sensor aimed at detecting smugglers and others entering the U.S. illegally. Ivie was shot and killed.
Another agent was shot in the ankle and buttocks but was released from the hospital after surgery. The third agent was uninjured.
Investigators trying to determine whether friendly fire occurred in a shooting involving law enforcement would compare the ballistics of officers' guns with bullet slugs that were either recovered from or passed through an officer's body, said David Klinger, a criminology professor at the University of Missouri at St. Louis and an expert in police shootings.
The officers involved in the case and any known witnesses also would be asked to provide accounts of such a shooting during interviews with investigators. And investigators would try to establish where officers and witnesses were positioned at the time of the shooting, Klinger said.
The Border Patrol couldn't immediately comment on the frequency of friendly fire shootings at the agency, but such incidents appeared to be extremely rare.
Ivie's death marked the first fatal shooting of an agent since a deadly December 2010 firefight with Mexican bandits that killed U.S. Border Patrol Agent Brian Terry and spawned congressional probes of a botched government gun-smuggling investigation.
Terry's shooting was later linked to that "Fast and Furious" operation, which allowed people suspected of illegally buying guns for others to walk away from gun shops with weapons rather than be arrested.