A church provides its minister a housing allowance, but for other purposes it believes that it must report the full amount of compensation (including the non-taxable housing allowance portion) on Form 1099-MISC (in order to demonstrate the full earnings of the minister). If the church reports his compensation, including the housing allowance, on Form 1099-MISC as taxable income, will he be able to deduct his housing expenses somewhere else on the Form 1040?
This questions brings up a couple of issues. First, most ministers are properly classified as employees who receive Form W-2, not as independent contractors who receive Form 1099-MISC. On Form W-2, Box 1 for taxable compensation is reduced reflecting the church's designation of a portion of his pay as non-taxable. Then in Box 14, it typically reports as a memorandum item his additional non-taxable, housing allowance compensation. In the situation addressed in the question, this Form W-2 reporting may or may not adequately address the other uses the church must make of the Form 1099-MISC.
Alternatively, the minister will need to report the full Form 1099-MISC income on Schedule C where it will be fully taxable. The minister could then claim as a deduction on Line 21 of his Form 1040 as Other Income a negative amount for his allowable housing allowance. He should probably attach an explanation of the negative amount and be ready to answer correspondence from the IRS regarding the deduction.
Of course, the full amount of compensation (including the non-taxable housing allowance) is subject to self-employment tax on Schedule SE unless the minister has successfully applied for exempt status using Form 4361.