National Transportation Safety Board Reauthorization Act of 2006

National Transportation Safety Board Reauthorization Act of 2006 - (Sec. 2) Amends federal transportation law to require a certain National Transportation Safety Board (NTSB) annual transportation accident investigation report to Congress to include: (1) a description of NTSB Academy activities and operations; (2) a list of transportation accidents during the prior calendar year that the NTSB did not investigate, including an explanation of why they were not investigated; and (3) a list of ongoing transportation accident investigations that have exceeded the time for completion by NTSB order, including an explanation for the additional time required to complete such investigations.

Directs the NTSB to develop, and submit to the Comptroller General and Congress, a plan for the NTSB Academy to achieve, to the maximum extent feasible, self-sufficiency and utilize fully the Academy's facilities and resources. Makes permanent the requirement of the Secretary of Transportation to submit a report to Congress and the NTSB containing the regulatory status of each NTSB recommendation made to the Secretary that is on the NTSB's "most wanted list" and requires the NTSB to review the Secretary's report and transmit comments to the Secretary and the congressional transportation committees.

(Sec. 3) Amends the National Transportation Safety Board Reauthorization Act of 2003 to: (1) make permanent the authority of the NTSB to enter noncompetitive contracts for the investigation of accidents; and (2) require annually, (currently, on February 1, 2006) as part of its transportation accident investigation report a report to the congressional transporation committees that describes each noncompetitive accident investigation contract for $25,000 or more executed by the NTSB and explains the rationale for dispensing with competition with respect to each such contract.

(Sec. 4) Authorizes appropriations to the Secretary for use by the Inspector General of the Department of Transportation (DOT) to cover expenses related to the prevention and detection of fraud and abuse in, and review of the financial management, property management, and business operations of, the NTSB.

(Sec. 5) Directs the Comptroller General of the United States to evaluate and audit NTSB programs and expenditures.

(Sec. 6) Requires the NTSB to continue to develop and implement internal audit controls for its operations.

(Sec. 7) Directs the Administrator of the Federal Aviation Administration (FAA) to report to Congress on why the FAA has not implemented the aviation recommendations in the NTSB's "Most Wanted Transportation Safety Improvements, 2006".

(Sec. 8) Extends the authorization of appropriations for the NTSB through FY2008. Authorizes the NTSB to impose and collect fees, refunds, and reimbursements for services provided by it (under current law, the NTSB can impose and collect fees for services provided by the NTSB Academy).

(Sec. 9) Requires, in addition to current related requirements, the NTSB to establish staffed bureaus, divisions, or offices to investigate and report on accidents involving marine transportation.

Grants the NTSB the authority to investigate major marine casualties occurring on or under all internal U.S. waters, in addition to the current authority to investigate on U.S. navigable waters or territorial seas. Grants the Secretary of the department in which the Coast Guard is operating the authority to investigate transportation accidents not involving government misfeasance or nonfeasance.

Grants authority to: (1) the Chairman of the NTSB to appoint non-regular and non-full-time employees in the immediate offices of another NTSB member; and (2) NTSB members to select and supervise regular and full-time employees in their immediate office (under current law, the Chairman has the authority to appoint and supervise such employees).

Directs the NTSB to develop and approve a process for the NTSB's review and comment or approval of documents submitted to the President, Director of the Office of Management and Budget (OMB), or Congress. Directs the NTSB to maintain at least one full-time employee in each state located more than 1,000 miles from the nearest NTSB regional office to provide initial investigative response to accidents investigated by the NTSB.

(Sec. 10) Requires the Secretary, with respect to the environmental review of a project to improve runway safety areas on Runway 8/26 at Juneau International Airport, Alaska, to only select as the preferred alternative the least expensive runway safety area alternative.

(Sec. 11) Directs the Inspector General of the DOT to provide oversight of activities performed by the Federal Highway Administration, the Massachusetts Executive Office of Transportation, and the Massachusetts Department of Transportation for the project-wide safety review initiated as a result of the July 10, 2006, accident in the Central Artery tunnel project in Boston, Massachusetts. Requires the Inspector General to: (1) investigate criminal or fraudulent acts committed in the design, expenditure of funds, and construction of such project; and (2) report periodically to Congress on such oversight and investigative activities.