Iran and Syria Nonproliferation Enforcement Act of 2006 - Amends the Iran and Syria Nonproliferation Act respecting the imposition of sanctions under such Act to: (1) apply sanctions for a minimum two-year period; (2) apply sanctions to an identified foreign person, a successor or subsidiary, and an entity controlling more than 50% of such foreign person, successor, or subsidiary (currently, such provision applies only to a foreign person); (3) include among applicable sanctions under Executive Order 12938 certain exemptions for military, medical, or humanitarian purposes; (4) establish investment, financing, and financial assistance prohibitions; and (5) require publication of sanctions applicable to such expanded entities in the Federal Register.
Authorizes the President to waive, with congressional notification, the imposition of any sanction for national security purposes.