"While it is important to emphasize that the FBI's investigation is actively continuing, there are strong preliminary indications that the death of United States Border Patrol Agent Nicholas J. Ivie, 30, and the injury to a second agent was the result of an accidental shooting incident involving only the agents," James Turgal, special agent in charge of the FBI's Phoenix division, said in a statement.
Ivie, a married father of 2, died in the shooting.
A second agent was shot in the ankle and buttocks and released from the hospital after undergoing surgery.
The third agent wasn't injured.
Authorities believe that the two agents exchanged gunfire in the mistaken belief that each was being fired on by a hostile gunman.
Ivie is the 14th agent killed in the line of duty since 2008, including three this year.
He was killed near a border station recently named for Brian Terry, whose 2010 death led to the public disclosure of the botched Fast and Furious gun-smuggling sting, according to Sen. Chuck Grassley of Iowa.
No weapons have been found and no arrests have been made on either side of the border.