Church Plan Clarification Act of 2012 - Amends the Internal Revenue Code to declare that an organization otherwise eligible to participate in a church plan shall not be aggregated with another such organization and treated as a single employer with it unless: (1) one organization provides directly or indirectly at least 80% of the operating funds for the other one during the recipient organization's preceding tax year, and (2) there is a degree of common management or supervision between the organizations.
Preempts any state law which would directly or indirectly prohibit or restrict the inclusion in any church plan of an automatic contribution arrangement.
Excludes from gross income amounts attributable to transfers of and mergers of church plans that are maintained by the same church or convention or association of churches.
Allows church plans and their supporting organizations to invest plan assets in a group trust (as defined by Internal Revenue Service Revenue Rulings).