Department of Homeland Security Management and Operations Improvement Act of 2006

Department of Homeland Security Management and Operations Improvement Act of 2006 - Directs the Secretary of Homeland Security to: (1) take steps to control the costs of hiring, training, and deploying new Border Patrol agents and limit the FY2007 cost for each new agent to $150,000; and (2) actively consult with and fully inform the congressional homeland security committees regarding all activities and responsibilities within their jurisdictions. Makes the Department of Homeland Security's (DHS) Inspector General independently responsible for keeping such committees informed.

Establishes in DHS a Directorate for Policy, Planning, and International Affairs, headed by an Under Secretary for Policy. Establishes within the Directorate an Office of International Affairs. Makes the Secretary, acting through the Under Secretary for Management, responsible for the integration and consolidation of DHS's management systems.

Directs the Inspector General to review each contract action related to DHS's Secure Border Initiative valued at greater than $20 million.

Requires the Chief Financial Officer to establish the Authorization Liaison Officer position.

Increases the number of federal annuitants who may be appointed by the Federal Law Enforcement Training Center.

Sets forth provisions regarding: (1) officials responsible for coordinating disability issues; and (2) homeland security procurement training.

Directs the Comptroller General to conduct a national study regarding emergency shelter accessibility and a study of the integration and adequacy of training for DHS personnel who process asylum seekers at U.S. ports of entry.

Requires the Secretary to: (1) establish a database of small business concerns, a Council on Procurement Training, a National Homeland Security University, and a Homeland Security Canine Detection Accreditation Board; and (2) increase the number of and coordinate DHS canine detection teams.