I would not check the box that the individual is exempt from SE tax because he is a minister because that is not a true statement... You may want to ask the client if he wishes to mail the return in via USPS certified mail with return receipt , then you can attach the documentation showing that he is exempt from self-employment tax as a U.N. employee... It may take longer to process but at least you will know that you have done the right thing .... This is just my opinion