New Markets for State-Inspected Meat and Poultry Act of 2006

New Markets for State-Inspected Meat and Poultry Act of 2006 - Directs the Secretary of Agriculture to review each state's meat and poultry inspection program, which shall include: (1) a determination of plan effectiveness; and (2) identification of changes necessary for future transition to a state program as provided for by this Act.

Rewrites and renames title III (currently titled,"Federal and State Cooperation") of the Federal Meat Inspection Act as "State Meat Inspection Programs."

Authorizes the Secretary to approve a qualifying state meat inspection program and allow the shipment in commerce of carcasses, parts of carcasses, meat, and meat food products so inspected. Requires the Secretary to review approved plans annually.

Authorizes the Secretary to: (1) enter into a cooperative agreement to establish the relationship between a state program and the Secretary; (2) provide partial reimbursement for state costs to meet federal requirements; and (3) appoint advisory committees.

Prohibits from state inspection plan participation establishments that have more than 50 employees, except for those subject to state inspection as of 90 days after the effective date of this Act.

Authorizes the Secretary to temporarily suspend or take over a noncomplying state program (or an establishment).

States that: (1) an establishment in a state with an approved state program may apply for either state or federal inspection; and (2) a state or local government shall not prohibit or restrict the movement or sale of meat or meat food products that have been inspected and passed in accordance with this Act for interstate commerce.

Exempts from such inspection provisions retail stores and restaurants (including specified central kitchen facilities) if the operations are conducted for sale of such prepared articles in normal retail quantities or for service of the articles to consumers at such establishment.

Makes similar amendments to the Poultry Products Inspection Act.