WASHINGTON (Reuters) - The Transportation Department said on Monday that it was investigating a whistle-blower complaint that aviation regulators allegedly covered up security shortfalls at U.S. airports for years. The inspector general's office confirmed that it was looking into the matter, but a spokesman would not comment on what steps investigators planned to take or how long their probe was likely to last. A veteran Federal Aviation Administration special agent who tested airport security alleges that senior officials at the agency were aware of airport security vulnerabilities but never corrected them. The agent also claimed that superiors tried to "bury" information about security problems without knowing if the deficiencies were ever corrected. FAA officials were not available to comment on the assertions, which were first reported by USA Today. The agency that evaluates whistle-blower cases for possible investigation, the office of special counsel, referred the complaint to transportation officials. The referral means that the special counsel believes the claim may have merit. The inspector general's findings must be reported back to the special counsel, which forwards the report to the White House and Congress. Until this month, the FAA and the airlines shared responsibility for aviation security. The FAA set guidelines and policies and judged threats. A central component of that responsibility was to test airlines to make sure they complied with government standards. For years, federal auditors raised numerous concerns with Congress about FAA oversight of security operations run by the airlines at hundreds of airports. For example, the Transportation Department inspector general's office found that little, if any, progress was made between 1993 and 1999 to improve FAA oversight of programs to regulate access to secure areas at airports. Audits found FAA slow to take action and was not aggressive enough when it did. The Sept. 11 hijack attacks prompted Congress to strip the FAA and the airlines of their airport security functions and turn them over to a new agency, the Transportation Security Administration. That agency will eventually run a passenger and baggage screening force of more than 30,000 people as well as oversee other critical areas of airport security. However, the TSA said this month that it would not extend whistle-blower protections to those government employees who disclose waste, fraud and abuse of authority in the work place. Such protection, the agency believes, could compromise aviation security.