Secure America Port Accountability Act of 2006 - Directs the Comptroller General to conduct a study, and report to Congress, on: (1) the extent to which security operations at U.S. seaports are managed by nationals of foreign countries; (2) any incident in which such foreign nationals have been charged with, or convicted of, a crime involving security operations at a U.S. seaport; (3) a review of U.S. contracts to manage or supply U.S. seaports, taking effect after December 31, 2001, with respect to the vulnerability of such seaports to threats to U.S. national security; and (4) a review of the vulnerability of the ten largest U.S. seaports to threats to the U.S. homeland security, including threats involving enemy infiltration, cargo shipping, and passenger safety, among others.