Church Plan Clarification Act of 2009

Church Plan Clarification Act of 2009 - Amends Internal Revenue Code pension plan provisions to: (1) apply a special rule for determining the status of an employer participating in a church plan as a member of a controlled group of entities; and (2) allow certain tax-free transfers to and mergers of church plans that are maintained by the same church or association of churches.

Amends the Tax Equity and Fiscal Responsibility Act of 1982 (TEFRA) to apply limitations on benefits and contributions under qualified employee plans to certain church defined benefit plans.

Includes within the definition of plan under the Employee Retirement Income Security Act of 1974 (ERISA) an employee benefit plan which is a church plan for purposes of ERISA automatic enrollment provisions.

Allows church plans and their supporting organizations to invest plan assets in a group trust (as defined by Internal Revenue Service Revenue Rulings).