Snowden left the CIA to become a contractor for the National Security Agency, and four years later leaked thousands of classified documents.
His supervisor's note and the CIA's suspicions apparently weren't sent to the NSA or its contractors, surfacing only after federal investigators began probing Snowden's record once the documents were leaked, intelligence and law enforcement officials told the New York Times in an article published Friday.
The supervisor's report "slipped through the cracks," one law enforcement official said.
Spokesmen for the CIA, FBI and NSA declined to comment on nature of the warning and why it was not forwarded.
Looking back, the CIA supervisor's report and the agency's suspicions may have been the first serious warnings about Snowden's eventual leaks, officials said.
"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," a Republican lawmaker briefed on Snowden's activities told the Times.
After leaking information about the NSA's massive cellphone and Internet monitoring program in May, Snowden holed up in Hong Kong before fleeing to Russia, which granted him temporary asylum of up to a year in July.
NSA Director Gen. Keith Alexander said Thursday Snowden's leaks would put people in harm's way, The Wall Street Journal reported.
Alexander's comments came hours after four former U.S. national security officials said they gave Snowden an award in Russia for "truth-telling."
"[Terrorists] listen, they see what has come out in the press and they adjust," Alexander told a business group focused on national security meeting in New York.
The damage caused by the leaks is irreversible, he told the Business Executives for National Security at its 2013 New York Eisenhower Award Dinner.
"I believe people will die because we won't be able to stop some of those threats," he said.
Alexander's comments came hours after the former U.S. intelligence officials -- whistle-blowers from the NSA, FBI, CIA and Justice Department -- said they presented the Sam Adams Award to Edward Snowden for "truth-telling" the night before.
The former officials -- Coleen Rowley, Thomas Andrews Drake, Ray McGovern and Jesselyn Radack, all members of the Sam Adams Associates for Integrity in Intelligence, made up of former national security officials -- told Russia's government-backed RT news channel Snowden appeared in good spirits.
Snowden's father, Lon Snowden, arrived in Moscow Thursday, saying he hoped to see his son, adding that his son may never return to the United States.
When he spoke to the media at Sheremetyevo International Airport, Lon Snowden was accompanied by Anatoly Kucherena, Edward Snowden's Kremlin-connected attorney, and the elder Snowden's official host.
"I'm here to learn more about my son's situation," Snowden said, "and I'm thankful, extremely thankful, to the Russian people, President Vladimir Putin and Mr. Kucherena and his staff for the help they have provided my son in terms of keeping my son safe and secure."