National Capital Transportation Amendments Act of 2006 - Amends the National Capital Transportation Act of 1969 to authorize the Secretary of Transportation to provide additional funding through grants to the Washington Metropolitan Area Transit Authority (WMATA) to finance in part the capital and preventive maintenance projects included in the Capital Improvement Program. Sets forth certain limits on the use of such grants. Prohibits funding to WMATA until it notifies the Secretary that certain amendments to the Washington Metropolitan Area Transit Authority Compact have taken effect.
Authorizes appropriations for such grants in an amount made available to the Secretary of the Treasury to make certain payments to the WMATA under the Outer Continental Shelf Lands Act.
Establishes within WMATA the Office of Inspector General. Sets forth the duties of the Inspector General, including to investigate complaints of activities constituting violations of law, rules, or regulations, or mismanagement, gross waste of funds, abuse of authority, or a substantial and specific danger to the public health and safety.
Sets forth certain prohibitions, conditions, and restrictions on the disposition or development of certain real properties by WMATA.
Requires the Comptroller General to study and report to Congress on the use of funds provided under this Act.