In 1984, Congress passed the Church Audit Procedures Act (CAPA) which gave several rules that the IRS must follow when auditing churches. It was passed to protect the constitutional rights of the churches.
One of the rules of the CAPA is that in order for the IRS to go ahead with any planned audit of any church, first the audit must have been approved by an IRS official at the level of Regional Commissioner or above.
However, in 1998, Congress reorganized the IRS and the regional structure of the IRS became divisional so there were no more Regional Commissioners. The IRS then designated the Director of Examinations in its Exempt Organizations division to fulfill the CAPA requirements.
However, in 2009 a Minnesota church, while it was being audited by the IRS, challenged the audit. The church complained that the IRS was not in compliance with CAPA regulations and didn’t have sufficiently high level official approval to conduct church audits. The IRS stopped auditing the church when a federal district court agreed with the church. - Christian Blog