Security managers can play an important role in advising employees with clearance problems, and can often save the company a valued employee or applicant which it otherwise might lose

        Although the vast majority of employees have no clearance problems, a small number are challenged by the Defense Investigative Service (DIS) and are eventually referred to the Defense Office of Hearings and Appeals (DOHA) for adjudication.

        The areas most likely to cause security clearance concerns are alcohol consumption, drug involvement, financial instability or carelessness in adhering to security regulations.

        Issues such as allegiance to the United States, foreign preference, outside activities or deliberate security violations rarely come into play at the administrative level because such conduct generally results in criminal prosecutions for subversion or espionage falling under the jurisdiction of the FBI and Department of Justice.

        If an employee’s clearance is brought into question, there are a number of steps he or she can take in defense both during the DIS investigation and later if referred to DOHA for adjudication. During the investigation, although an employee must cooperate and to speak with a DIS investigator, he has the right to have an attorney present at the interview.

        During the investigation an employee may also be asked to take a polygraph examination and at its conclusion also asked to give a signed sworn statement of what he said during the examination. For clearances at the confidential, secret and top secret level, an employee may refuse to take a polygraph examination and that may not be used against him in determining whether to grant the clearance. (For SAP and SCI access an employee must agree to be polygraphed).

        If an employee does agree to take a polygraph, he has the right to have an attorney present at the polygraph, to consult with the attorney during the polygraph and to discontinue the polygraph at any time. At the conclusion he has the right to decline to give a written sworn statement of what he said.

        If DIS refers the case to DOHA for adjudication the employee will be sent a "Statement of Reasons" which is a mixed statement of factual allegations and legal conclusions, and the employee must reply under oath within 20 days either admitting or denying the charges.

        The charges are frequently restated in multiple ways and invariably include a catch-all charge of "conduct involving questionable judgment, untrustworthiness, unreliability or unwillingness to comply with rules and regulations."

        Even if the employee is exonerated of the underlying misconduct, the security clearance may still be revoked because of "poor judgment or unreliability."

        In replying to the Statement of Reasons an employee will frequently admit to everything without focusing on the facts alleged or the legal conclusions to be drawn. Although he may later attempt to amend his answer, his original reply will be considered as evidence against him.

        Though an employee may have committed the acts charged, that is only the beginning of the inquiry. The Adjudication Guidelines require the weighing of a number of variables known as the "whole person concept", which include the circumstances surrounding the conduct, the individual’s age and maturity, motivation and the possibility of rehabilitation.

        Once the government has presented its case, the employee has the burden of demonstrating that the granting of or continuing eligibility for a security clearance is "clearly consistent with the interests of national security." Any doubt will be resolved in favor of the "national security", i.e. to deny a clearance.

        After an initial decision by the DOHA Administrative Judge, either the government or the employee may appeal to the DOHA Appeals Board which will make a final determination based on the record of the hearing. Unless a constitutional issue is raised, which is rare, the decision of the Appeals Board will be final and not reviewable by a court.