As a result, the National Reconnaissance Office closely tracked how many personal confessions it collected. The agency called them “Code 55 admissions,” the records show.

In fiscal year 2011, almost 50 percent of the 757 confessions the agency collected were of the personal nature that the rules said shouldn’t be directly pursued, the agency’s statistics show. Of 33 polygraphers, one-third collected more confessions related to personal behavior than to national security violations.

Other polygraph programs, such as those in the Naval Criminal Investigative Service, also conduct limited national-security polygraph screenings, but in an entire year their polygraphers may not encounter any confessions that are outside the limits of the test. It’s a rare occasion when someone blurts it out without prompting, officials said.

“If an agency is getting a big portion of its confessions that are outside the limits, it’s an indication that they’re going on fishing expeditions,” said John Sullivan, a former CIA polygrapher of 30 years. “And if they’re doing that, it’s wrong and being done under false pretenses.”

Phillips and Hinshaw accused the polygraph program’s branch chief, McMahon, of encouraging improper practices.

Within the intelligence world, only the CIA and the National Security Agency are permitted to directly ask about drug use, unreported crimes and falsification of the forms filled out for national security clearances, which require a wide array of personal information. The tests are known as lifestyle polygraphs.

Late last year, the Pentagon discovered that the National Reconnaissance Office had ordered five of the lifestyle tests in violation of Defense Department policies, according to an internal report obtained by McClatchy. The agency then claimed to have the legal authority to do so, when it was supposed to be asking only national security questions designed to catch spies and terrorists, the report said. The Pentagon concluded that the program was in “full compliance” because the agency said it was a mistake.

Polygraphers, however, say the agency’s pursuit of the off-limits information is much more widespread than the Pentagon’s report noted. Records show that the agency ordered at least one more lifestyle test after it was told to stop.

The agency also pursues the information in its routine counterintelligence tests, polygraphers said. In one instance last year, Phillips’ supervisors told him to “assess” the mental health of an applicant during a polygraph test, records show. Phillips said he’d refused to do it.

As a result of its efforts, the agency ends up with a vast accumulation of personal details of questionable national-security significance, polygraphers said.

Last September, a woman who’d held a clearance for more than 15 years and already had passed a national security polygraph was interrogated for more than four hours over two additional polygraph sessions, said Hinshaw, who said he’d been ordered to do it. Hinshaw’s supervisors launched the aggressive inquiry because they suspected that the woman had smoked pot more than the one time years before that she’d admitted to, records show. In the end, however, the only other information the National Reconnaissance Office extracted from her was that she’d been molested at age 16.

Hinshaw said he’d received thousands of dollars in bonuses over several years in part because he’d collected a high number of confessions, including the more personal ones.

Phillips, on the other hand, had a much lower collection rate and received negative performance reviews. His supervisors cited his reluctance to collect the Code 55 information as part of the reason for their dissatisfaction with him.

“There are ways of leading people into making these admissions even though you’re not supposed to,” Phillips said. “By setting up a system that gives polygraphers an incentive to go after the information, the agency is pressuring them to collect it.”

Despite the agency’s interest in criminal behavior, those who confess to serious offenses aren’t always criminally prosecuted even when child molestation is involved, McClatchy found.

In one case, a contractor who was a former Escondido, Calif., substitute teacher admitted to molesting a third-grade student in 2005 during outside tutoring sessions paid for by the girl’s immigrant parents. In a 2010 polygraph session, the man said that if he were asked, “ ‘Have you ever molested a 9-year-old?’ I’d have to say yes.”

The Escondido Police Department and school district where he’d been employed weren’t notified of the incident. After being contacted by McClatchy, the school district called the Escondido Police Department to file a report.When National Reconnaissance Office polygraphers asked supervisors in a meeting last summer why people weren’t being arrested on the spot after such confessions, they were told that the allegations were referred to the appropriate authorities, Phillips and Hinshaw said.

The agency refused to answer McClatchy’s questions about the molestation confession, saying in a statement only that its polygraph program “is in compliance with the law.”

National Reconnaissance Office statement on its polygraph program

“The National Reconnaissance Office directs, manages and oversees appropriate investigative inquiries, including polygraph, for the purposes of rendering informed security access determinations. Such inquiries and determinations are in full compliance with the law and provide the security compliance required to best protect and further Intelligence Community program activities and objectives.

“If adverse information is disclosed during the administration of a polygraph examination the information is evaluated and forwarded to the appropriate authorities. For Privacy Act purposes the NRO has a policy of not commenting on specific cases.

“The National Center for Credibility Assessment (NCCA), Quality Assurance Program (QAP), conducted an on-site inspection of the NRO Polygraph Program on November 15-17, 2011. During the QAP inspection, 118 criteria in nine primary areas were reviewed. Upon conclusion of the inspection, the NRO Polygraph program was found to be in full compliance with their policies and procedures and met or exceeded all standards required of a federal government polygraph program.”

Tish Wells contributed to this article.