Homeland Security Information Sharing Enhancement Act of 2006

Homeland Security Information Sharing Enhancement Act of 2006 - Amends the Homeland Security Act of 2002 to require the Under Secretary for Information and Analysis to implement a Homeland Security Advisory System to provide advisories and alerts regarding threats to homeland security. Requires such an advisory or alert to: (1) include information on protective measures and countermeasures; (2) be limited in scope to a specific region, locality, or economic sector; and (3) not use color designations as the exclusive means of specifying threat conditions.

Directs the Secretary of the Department of Homeland Security (DHS) to: (1) integrate and standardize the information of the Department's intelligence components into a Department information-sharing environment; and (2) designate, for each such component, an information-sharing and knowledge management officer.

Requires the Under Secretary to: (1) establish Department-wide procedures for the review and analysis of information gathered from state, local, tribal, and private-sector sources; (2) develop mechanisms to provide analytical and operational feedback; (3) provide Department employees training and educational opportunities; and (4) evaluate how employees of the Office of Intelligence and Analysis and the Department's intelligence components are utilizing homeland security information.

Directs the Secretary, acting through the Chief Intelligence Officer, to establish a comprehensive information technology architecture for such Office.

Makes the Secretary the executive branch official responsible for disseminating homeland security-related terrorist threat information to state and local government and tribal officials and the private sector. Prohibits any federal official from issuing a homeland security-related analysis, advisory, or alert without the Secretary's approval, with exceptions.