Natural Disaster Housing Reform Act of 2006

Natural Disaster Housing Reform Act of 2006 - Makes the Department of Housing and Urban Development the primary federal agency responsible for coordinating and administering housing assistance in connection with any major disaster that will result in long-term housing needs.

Prescribes guidelines for the Secretary of Housing and Urban Development to implement such assistance.

Amends the Robert T. Stafford Disaster Relief and Emergency Assistance Act to direct the President, upon state request, to provide such housing assistance if the relevant major disaster will displace individuals or households from their predisaster primary residences, or will render such residences uninhabitable, for a period of 30 days or more.

Instructs the President, when making any cost effectiveness determination, to consider whether manufactured modular housing can be provided at a federal cost less than the same cost necessary to provide other readily fabricated dwellings.

Authorizes the President to provide financial assistance for: (1) the repair, to a safe and sanitary living or functioning condition, of existing rental units that will be used as alternate housing accommodations; and (2) permanent and semi-permanent housing construction in remote locations of declared major disaster or emergency in connection with Hurricane Katrina of 2005 during the period between August 28, 2005, and December 31, 2007.

Permits the location in a special flood hazard zone, under the Flood Disaster Protection Act of 1973, of any permanent, semi-permanent, or temporary housing, including any readily fabricated dwelling, manufactured housing, or manufactured modular housing.

Instructs the Director of the Federal Emergency Management Agency (FEMA) to develop detailed and comprehensive mass evacuation plans for individuals or households receiving assistance for the 18-month period following a disaster declaration.