National Defense Critical Infrastructure Protection Act of 2006

National Defense Critical Infrastructure Protection Act of 2006 - Prohibits a corporation from owning, or being authorized to manage or operate, any system or asset that is included on the national defense critical infrastructure list (list) unless the corporation meets specified critical infrastructure national security management requirements, including: (1) being organized under the laws of the United States; (2) having a board of directors the majority of whom are U.S. citizens; (3) having a chief executive officer and board chairman who are U.S. citizens; (4) having a majority of voting shares and nonvoting shares being owned by U.S. citizens; and (5) having more than 50 percent of the board members approved by the Secretary of Defense (Secretary), in consultation with the Secretary of Homeland Security. Requires any such corporation to promptly notify the Secretary of certain corporation acquisition, ownership or other control obtained by a foreign person.

Requires the Secretary to: (1) maintain such list; and (2) notify the congressional defense committees of any list revisions.

Amends the Defense Production Act of 1950 to provide for the confidentiality of information obtained during an investigation of corporate mergers, acquisitions, and takeovers (transactions) that may affect U.S. national security. Allows the President to suspend or prohibit a transaction if there is credible evidence that a foreign interest exercising control might take action that threatens to impair the national security or affect the ability of domestic industries to meet existing production requirements for defense or homeland security. Provides additional national security factors to be considered by the President when reviewing a proposed transaction, including defense production and potential effects on the control of critical infrastructure and access to strategic natural resources. Requires the President to be notified of a proposed transaction that may affect U.S. national security.

Prohibits any cargo transported by commercial motor vehicle from Canada or Mexico, and any cargo transported by vessel, from entering, or being unloaded in, the United States unless the appropriate officer or employee has inspected the cargo to ensure compliance with all U.S. laws.