Military Commissions Act of 2006

Authorizes the President to establish such commissions. Prohibits commission findings, holdings, and other precedents from being introduced or considered in any proceeding of a court-martial convened under the UCMJ. Prohibits a combatant subject to trial by commission from invoking the Geneva Conventions as a source of rights. Allows commissions to impose upon any person found guilty any punishment not forbidden under the UCMJ, including the death penalty. Requires an annual report from the Secretary to the congressional defense committees on any trials conducted.

Makes eligible to serve on a commission any commissioned officer of the Armed Forces on active duty. Requires to be detailed to each commission a military judge, trial and military defense counsel, and reporters and interpreters. Requires at least five members in each commission.

Outlines commission pre-trial procedures, including charges and specifications. Prohibits a person from being required to testify against himself (compulsory self-incrimination) at a commission proceeding. Prohibits (with a limited exception) a statement obtained by the use of torture from being admissible against the accused.

Prescribes commission trial procedures, including: (1) rules of evidence; (2) duties of trial and defense counsel; (3) pleas of the accused; (4) opportunity to obtain witnesses and other evidence; (5) the defense of lack of mental responsibility; and (6) the record of trial. Requires: (1) a two-thirds commission member vote for conviction; (2) a three-fourths member vote for a sentence of life imprisonment or confinement of more than ten years; and (3) a unanimous vote by at least 12 members in a case in which the death penalty is sought. Prohibits any sentence from including cruel or unusual punishments such as flogging, branding, or marking or tattooing of the body.

Prescribes commission post-trial procedures, including: (1) review by the convening authority; (2) appeal by the United States; (3) rehearings; (4) reviews by the Court of Military Commission Review, the U.S. Court of Appeals for the District of Columbia, and the U.S. Supreme Court; and (5) the execution of sentences.

Makes the following offenses triable by commissions: (1) murder of protected persons; (2) attacking civilians; (3) attacking civilian objects; (4) attacking protected property; (5) pillaging; (6) denying quarter; (7) taking hostages; (8) employing poison or similar weapons; (9) using protected persons as a shield; (10) using protected property as a shield; (11) torture; (12) cruel or inhuman treatment; (13) intentionally causing serious bodily injury; (14) mutilating or maiming; (15) murder in violation of the law of war; (16) destruction of property in violation of the law of war; (17) using treachery or perfidy; (18) improperly using a flag of truce; (19) improperly using a distinctive emblem; (20) intentionally mistreating a dead body; (21) rape; (22) sexual assault or abuse; (23) hijacking or hazarding a vessel or aircraft; (24) terrorism; (25) providing material support for terrorism; (26) wrongfully aiding the enemy; (27) spying; (28) conspiracy; (29) perjury and obstruction of justice; and (30) contempt.

Requires a report from the Secretary to the defense committees setting forth commission procedures prescribed under this Act.

(Sec. 4) Makes inapplicable to commissions UCMJ provisions concerning: (1) contempt; (2) speedy trial; (3) self-incrimination warnings; and (4) pretrial investigations.

(Sec. 5) Prohibits a person from invoking the Geneva Conventions in any habeas corpus or other civil action to which the United States, a current or former officer, employee, or member of the Armed Forces, or other agent of the United States is a party as a source of rights in any court of the United States or its states or territories.

(Sec. 6) Authorizes the President to interpret the meaning and application of the Geneva Conventions and to promulgate standards and regulations for violations of treaty obligations which are not grave breaches of the Geneva Conventions. Directs the President to issue such interpretations through Executive Orders.

Amends the federal criminal code to include the following as violations of the War Crimes Act: (1) torture; (2) cruel or inhuman treatment; (3) performing biological experiments; (4) murder; (5) mutilation or maiming; (6) intentionally causing serious bodily injury; (7) rape; (8) sexual assault or abuse; and (9) taking hostages.

Prohibits any person in the custody or control of the United States, regardless of nationality or physical location, from being subject to cruel, inhuman, or degrading treatment or punishment.

(Sec. 7) Amends federal criminal justice provisions to deny any court or judge jurisdiction to hear or consider an application for a writ of habeas corpus filed by or on behalf of, or to hear or consider any other action against the United States or its agents relating to any aspect of the detention, treatment, or trial of, an alien detained outside the United States who is or was detained by the United States and has been determined to have been properly detained as an enemy combatant or is awaiting such determination. Makes the provisions of this section effective upon enactment, and applicable to all cases, without exception, pending on or after enactment which relate to any aspect of the detention, transfer, treatment, trial, or conditions of detention of an alien detained by the United States since September 11, 2001.

(Sec. 8) Amends provisions of the Detainee Treatment Act of 2005 relating to the protection of U.S. government personnel engaged in authorized interrogations to: (1) require (currently authorizes) the U.S. government to provide counsel and pay the legal fees of any such personnel with respect to any civil action or criminal prosecution arising out of an authorized interrogation; and (2) make such provisions effective with respect to actions occurring between September 11, 2001, and December 30, 2005.

(Sec. 9) Amends the Detainee Treatment Act of 2005 to make reviews of all judgments of commissions (currently, only judgments involving a capital case or a case in which the alien was sentenced to imprisonment of ten years or more) a matter of right.

(Sec. 10) Includes all aliens detained by the United States (currently, only those detained by the Department of Defense at Guantanamo Bay, Cuba) under the authority for the review by the U.S. Court of Appeals for the District of Columbia of a decision of a Combatant Status Review Tribunal that an alien is properly detained as an enemy combatant.