The New York Times is out with a report that the Central Intelligence Agency warned that Edward Snowden might be a security risk some four years before he managed to abscond unknown amounts of intelligence data from the National Security Agency and leave the country:

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.

Half a dozen law enforcement, intelligence and Congressional officials with direct knowledge of the supervisor’s report were contacted for this article. All of the officials agreed to speak on the condition of anonymity because of the continuing criminal investigation.

In hindsight, officials said, the report by the C.I.A. supervisor and the agency’s suspicions might have been the first serious warnings of the disclosures to come, and the biggest missed opportunity to review Mr. Snowden’s top-secret clearance or at least put his future work at the N.S.A. under much greater scrutiny.

“The weakness of the system was if derogatory information came in, he could still keep his security clearance and move to another job, and the information wasn’t passed on,” said a Republican lawmaker who has been briefed on Mr. Snowden’s activities.

(…)

Intelligence and law enforcement officials say the report could have affected the assignments Mr. Snowden was given, first as an N.S.A. contractor with the computer company Dell in Japan and later with Booz Allen Hamilton in Hawaii, as well as the level of supervision he received.

The electronic systems the C.I.A. and N.S.A. use to manage the security clearances for its full-time and contracted employees are intended to track major rule-based infractions, not less serious complaints about personal behavior, a senior law enforcement official said. Thus, lesser derogatory information about Mr. Snowden was unlikely to have been given to the N.S.A. unless it was specifically requested. As a result of Mr. Snowden’s case, two law enforcement officials said, that flaw has since been corrected and such information is now being pushed forward.

The revelation of the C.I.A.’s derogatory report comes as Congress is examining the process of granting security clearances, particularly by USIS, a company that has performed 700,000 yearly security checks for the government. Among the individuals the company vetted were Mr. Snowden and Aaron Alexis, who the police say shot and killed 12 people at the Washington Navy Yard last month.

“We have a compelling need to monitor those trusted with this sensitive information on a more regular basis and with broader sets of data,” said Kathy Pherson, a former C.I.A. security officer who belongs to an intelligence industry task force that is expected to issue a report on the matter by year’s end.

While it is unclear what exactly the supervisor’s negative report said, it coincides with a period of Mr. Snowden’s life in 2009 when he was a prolific online commenter on government and security issues, complained about civil surveillance and, according to a friend, was suffering “a crisis of conscience.”

While it’s unclear that one derogatory report would have put Snowden’s security clearance at risk, the fact that it wasn’t communicated to the NSA arguably is in that it is yet another example of how cross-agency communication is far less than it should be. As the article notes, the problem also revealed itself in connection with the shooter at the Washington Navy Yard. Just months before the incident, Providence, R.I. police had reported to the Navy about the fact that he was talking about hearing voices and apparently voicing paranoid delusions. For reasons that are still unclear, that information was not passed on to either the contractor that he was working for, or to the facility where he was next being sent, and where he ultimately caused needless death and injury. Obviously, some re-examination of this entire system is needed.