Brian Patrick O' Callaghan, 36, of Damascus, was the chief of the National Security Agency's Korea division when he was arrested on Feb. 16, officials told CBS News.
O'Callaghan was charged with first-degree murder and child abuse in the death of his son, Hyunsu O'Callaghan, who died Feb. 3.
A medical examiner ruled that the child's death was caused by multiple blunt force injuries.
O'Callaghan told police the child had slipped in the bathtub on Jan. 31 and fell backward, hitting his shoulder.
Hyunsu was unresponsive when his father took him to an emergency room. His injuries indicated the boy had recently been beaten, doctors told police.
"These types of injuries are consistent with acute head trauma and Brian O'Callaghan could not provide an explanation that would cause this type of medical distress to Hyunsu," a document stated.
The boy's injuries included a skull fracture with bleeding in the brain and his body showed multiple contusions, CBS reported.
O'Callaghan was being held without bail.
His attorney, Steven McCool, said the death of the boy was a tragedy, but not a crime.
"[O'Callaghan] has the unwavering support of his family; they know he is incapable of committing the crimes alleged," McCool said.
The boy was adopted from Korea and has been in the United States since October 2013.