Mark-to-Market Extension Act of 2006

Mark-to-Market Extension Act of 2006 - (Sec. 2) Amends the Multifamily Assisted Housing Reform and Affordability Act of 1997 to reauthorize to October 1, 2011: (1) the Mark-to-Market program; and (2) provisions of the FHA-insured Multifamily Housing Mortgage and Housing Assistance Restructuring program regarding projects and programs for which binding commitments have been entered into under such Act.

(Sec. 3) Permits the Secretary of Housing and Urban Development to waive rent level limits for up to 9% (currently 5%) of all units subject to restructured mortgages in any fiscal year, based on certain findings of special need.

(Sec. 4) Revises requirements for an approved mortgage restructuring and rental assistance sufficiency plan with respect to modification or forgiveness of all or part of a second mortgage held by the Secretary (debt relief) if the project concerned is acquired by a tenant organization or tenant-endorsed community-based nonprofit or public agency.

Sets forth requirements for alternative periods of eligibility for such nonprofit debt relief if the purchaser acquires the project subsequent to the date of recordation of the related affordability agreement, and two years after the date of enactment of this Act.

(Sec. 5) Declares disaster-damaged eligible projects eligible without regard to the relationship between rent level for the assisted units and comparable market rents.

(Sec. 6) Requires each mortgage restructuring and rental assistance sufficiency plan to determine for units assisted with project-based assistance in eligible multifamily housing projects, if rents cannot be determined, adjusted rent levels: (1) for disaster-damaged eligible projects equal to 100% of the fair market rents for the relevant market area; and (2) for other eligible multifamily housing projects equal to 90% of the fair market rents for the relevant market area.

States that, with respect to a disaster-damaged eligible project, the owner contribution toward rehabilitation needs shall be determined in accordance with specified requirements.