Al-Qaeda and other hostile groups have repeatedly sought to infiltrate US intelligence agencies, which are investigating thousands of their employees to counter the threat, The Washington Post reported on Monday.
The CIA found that about a fifth of job applicants with suspect backgrounds had "significant terrorist and/or hostile intelligence connections," the Post cited a classified budget document as saying.
The document was provided to the paper by former National Security Agency contractor Edward Snowden, now a fugitive in Russia under temporary asylum.
Although the file did not describe the nature of the jobseekers' extremist or hostile ties, it cited Hamas, Hezbollah and Al-Qaeda and its affiliates most often.
The fear of infiltration is such that the NSA planned last year to investigate at least 4,000 staff who obtained security clearances.
The NSA detected potentially suspicious activity among staff members after trawling through trillions of employee keystrokes at work.
The suspicious behavior included staffers accessing classified databases they do not usually use for their work or downloading several documents, two people familiar with the software used to monitor staff told the Post.
But serious delays and uneven implementation have hit the multimillion-dollar effort, and the spy agencies never detected Snowden copying a wide range of the NSA's highly classified documents.
The fugitive leaker is wanted by Washington on espionage charges linked to media disclosures about US surveillance programs.
"Over the last several years, a small subset of CIA's total job applicants were flagged due to various problems or issues," one official told the Post.
"During this period, one in five of that small subset were found to have significant connections to hostile intelligence services and or terrorist groups."
The NSA is also creating a huge database known as WILDSAGE to help share sensitive intelligence among cybersecurity centers, according to the budget document. But the move has raised concern that the database could be infiltrated.
Intelligence agencies have stepped up scrutiny of insider threats following the disclosure of hundreds of thousands of military and diplomatic files by WikiLeaks in 2010.
Army Private Bradley Manning, an intelligence analyst now known as Chelsea Manning, had leaked the documents to the anti-secrecy group.
In 2011, Congress ordered Director of National Intelligence James Clapper to set up an "automated insider threat detection program" to prevent further such leaks, stop possible abuses and identify double agents.
But the project was delayed several times as the intelligence community dealt with the aftermath of Manning's leaks, the Post said.
President Barack Obama's administration has cracked down on insider threats.
In November 2012, Obama issued a National Insider Threat Policy that defined the threats as coming from "espionage, terrorism (or) unauthorized disclosure of national security information."
The policy places whistleblowers, spies and "terrorists" in a single category, and has triggered outcries from critics who say the three are distinct.