In a letter to union members Jesse Sekhon says there has been a "vacuum of leadership" under Chief Gary Gee.
He went on to say that he understands the frustration with the lack of direction and leadership in BART's management.
BART responded to the statement only by saying it is conducting a complete and thorough investigation of the deadly New Year's Day shooting.
The former officer charged in Oscar Grant's death, Johannes Mehserle, remains in Dublin's Santa Rita jail.
