There is a new version of IRS Publication 517, Social Security and Other Information for Members of the Clergy and Religious Workers, on the IRS website.
The Publication includes a chart (Table 1) on whether ministers, members of a religious order who have taken (or not taken) a vow of poverty, Christian Science practitioners, church employees, and members of a recognized religious sect are subject to FICA tax. If these individuals are not subject to FICA tax, they should file Form 4029, Application for Exemption From Social Security and Medicare Taxes and Waiver of Benefits, with the IRS. An employer is advised not to report wages paid to these individuals as Social and Medicare wages if the individual has provided the employer with an approved Form 4029. Employers completing a Form W-2 for an employee with an approved Form 4029 should enter “Form 4029” in box 14, “Other.”
Employers should not make any entries for ministers in boxes 3, 4, 5, or 6 of Form W-2. Employers should also not include exempt wages for an employee with an approved Form 4029 on Forms 941, 943, and 944. Instead, Form 941 filers are advised to check the box on line 4 (“no wages, tips, and other compensation are subject to Social Security or Medicare tax”) and enter “Form 4029” in the empty space below the check box for Form 941. Form 943 filers should enter “Form 4029” to the right of the wage entry spaces on lines 2 and 4 of Form 943. Form 944 filers should check the box on line 3, and enter “Form 4029” in the empty space below the check box. Publication 517 for use in preparing 2011 returns can be viewed on the IRS website at http://www.irs.gov/pub/irs-pdf/p517.pdf.