"The CIA found that among a subset of job seekers whose backgrounds raised questions, roughly one out of every five had significant terrorist and/or hostile intelligence connections," The Washington Post said, citing a classified budget document provided by former National Security Agency contractor Edward Snowden.
The groups cited most often were Hamas, Hezbollah, and al-Qaeda and its affiliates, but the nature of the connections was not described in the document, the paper said.
"So sharp is the fear of threats from within that last year the NSA planned to launch at least 4,000 probes of potentially suspicious or abnormal staff activity after scrutinising trillions of employee keystrokes at work.
"The anomalous behaviour that sent up red flags could include staffers downloading multiple documents or accessing classified databases they do not normally use for their work, said two people familiar with the software used to monitor employee activity," the Post said.
"This shrouded, multimillion-dollar hunt for insider threats has suffered from critical delays in recent years and uneven implementation across agencies, the budget records show. And the spy agencies' detection systems never noticed that Snowden was copying highly classified documents from different parts of the NSA's networks," the paper said.
Contractors like Snowden, who leaked some of America's most closely guarded secrets, were not included in the plans to reinvestigate 4,000 security clearances, the paper said.
Snowden subsequently fled to Hong Kong and then Moscow, where he remains after being granted temporary asylum.
CIA officials said the number of applicants ultimately tied to terrorist networks or hostile foreign governments was 'small' but declined to provide an exact number or the reasons the broader group of applicants initially raised concerns.
The intelligence community's dramatic emphasis on insider threats came in the wake of disclosures by WikiLeaks in 2010.
The anti-secrecy group received hundreds of thousands of military and diplomatic documents from convicted American soldier Bradley Manning, the paper said.