Your posting is a little confusing, however, if the school is an integral agency of a church, and it probably is, it would be able to treat an employee performing ministerial duties as a dual status minister for tax purposes and designate a parsonage allowance if it meets most of the requirements of RR 72-606 to be an integral agency of a church.
RR 70-549 and RR 72-606 clearly state what is requireed to a school, mission, or other religous organizatioin to be under the control of a church and qualify as an integral agency of a church.
If all qualifies, you would handle him like any other pastor. If it doesn't, the housing allowance becomes taxable.
This can be a tricky area, however, my guess is, that if you contact the school, they may have documentation showing qualification, maybe even a PLA.
Now, let me explain your problem, as I see it. You are indicating that he received a normal W-2, that is, one that has FICA and Medicare deducted on it. If that is the case, he does not qualify for a housing allowance because that would indicated that he does not have dual status. If the W-2 is issued in error that way, you would need to have the W-2 corrected.
I do not now all the answers, however, I do specialize in clergy taxes and would be happy to help you with any questions that I can. You can contact me directly at
[email protected]. You should note, that if you contact me directly, you will receive the benefit of peer review that this board makes available.
I hope this has helped.
Mike