9-11 Commission Combating Proliferation Implementation Act

9-11 Commission Combating Proliferation Implementation Act - Establishes within the Executive Office of the President the Office for Combating the Proliferation of Weapons of Mass Destruction (WMDs). Requires the Director of the Office to: (1) develop and advise the President on WMD anti-proliferation policies; and (2) implement a Strategy for Combating the Proliferation of WMDs.

Expresses the sense of Congress that: (1) the President should request the President of the Russian Federation to appoint a corresponding official to the Director; (2) the President should expand and strengthen the Proliferation Security Initiative (PSI); and (3) the United States should engage the United Nations to develop a U.N. Security Council resolution authorizing the PSI under international law.

Authorizes funding for: (1) acceleration of removal or security of fissile materials, radiological materials, and related equipment at vulnerable sites worldwide; (2) joint training exercises regarding interdiction of weapons of mass destruction under the PSI; and (3) Cooperative Threat Reduction programs (CTR).

Gives the President permanent waiver authority over provisions prohibiting the use of certain CTR funds for chemical weapons destruction facilities in Russia.

Amends the National Defense Authorization Act for Fiscal Year 2004 to repeal specified CTR fund limits for activities outside the former Soviet Union.