"It was either accidental or target misidentification," Alameda County Sheriff's Sgt. J.D. Nelson said.
The shooting, which occurred about 1:45 p.m. PST while several officers were conducting a probation search of a robbery suspect's apartment, was the first on-duty death in the history of the BART Police Department, the San Francisco Chronicle reported.
The shooting occurred after the suspect had been taken into custody.
Nelson said the dead officer had been on the force for 20 years and the officer who shot him has been with the department for a decade.
The newspaper said sources it described as familiar with the investigation said the dead officer was Sgt. Tom Smith, 42, a married father of one.
The sources said Smith's wife also is a BART officer and he has a brother who is an Alameda County sheriff's deputy.