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.

Spokesmen for the C.I.A., N.S.A. and F.B.I. all declined to comment on the precise nature of the warning and why it was not forwarded, citing the investigation into Mr. Snowden’s activities.