Agriculture Small Business Opportunity and Enhancement Act of 2006 - Amends the Federal Meat Inspection Act to authorize the Secretary of Agriculture 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. Prohibits from state inspection plan participation: (1) establishments that have more than 50 employees, except for those subject to state inspection as of January 1, 2007; and (2) federally inspected establishments after such date that have more than 50 employees. Authorizes the Secretary to: (1) enter into a cooperative agreement to establish the relationship between a state program and the Secretary; and (2) provide partial reimbursement for state costs to meet federal requirements. Sets forth provisions with respect to: (1) sampling; (2) noncompliance; (3) acceptance of interstate shipments of meat and meat food products; and (4) advisory committees. Directs the Secretary to temporarily suspend or take over a noncomplying state program (or an establishment). Makes similar amendments to the Poultry Products Inspection Act. Terminates the Secretary's authority to establish interstate meat and poultry inspection programs under this Act if approval and cooperative agreements have not been concluded by January 1, 2007.
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