As investigators continue to delve into the weeks and months prior to Snowden’s defection with thousands of classified documents, a lot of critics of government contractors have argued that Booz Allen failed to pay attention to some very troubling warning signs when they hired him. It seems that the most visible warning signs never showed up because the CIA failed to report them.

WASHINGTON — Just as Edward J. Snowden was preparing to leave Geneva and a job as a C.I.A. technician in 2009, his supervisor wrote a derogatory report in his personnel file, noting a distinct change in the young man’s behavior and work habits, as well as a troubling suspicion.

The C.I.A. suspected that Mr. Snowden was trying to break into classified computer files to which he was not authorized to have access, and decided to send him home, according to two senior American officials.

But the red flags went unheeded. Mr. Snowden left the C.I.A. to become a contractor for the National Security Agency, and four years later he leaked thousands of classified documents. The supervisor’s cautionary note and the C.I.A.’s suspicions apparently were not forwarded to the N.S.A. or its contractors, and surfaced only after federal investigators began scrutinizing Mr. Snowden’s record once the documents began spilling out, intelligence and law enforcement officials said.

“It slipped through the cracks,” one veteran law enforcement official said of the report.

More: C.I.A. Warning on Snowden in ‘09 Said to Slip Through the Cracks