Wheat Counter-Cyclical Payments Enhancement Act of 2006 - Amends the Farm Security and Rural Investment Act of 2002 to authorize the Secretary of Agriculture to consider national average market price variations for different classes of wheat (including soft white wheat) when determining wheat producer eligibility for 2005-2007 counter-cyclical payments.
States that in calculating a separate effective price for a class of wheat the effective price shall equal the sum of: (1) the higher of the national average market price received by producers during the 12-month marketing year, or the national average loan rate during that period; and (2) the direct wheat payment rate.