If you are a clergy member of the church, then any money the church directly pays to you is considered part of your wages and should be reported in box 1 of your W-2. Your employer can't give you tax-free gifts, it's just not allowed, even for clergy. Tell the church they need to cancel the 1099-NEC and issue a corrected W-2.
If you are not a regular employee of the church, you might be a self-employed missionary. The income is still taxable and a 1099-NEC is appropriate.
The way to receive a tax-free gift is to have it come directly from the parishioners or church members into your pocket, and not through the church. (However, those gifts will not be tax deductible to the giver, since personal gifts are never tax deductible.) Once the church gets involved and it goes through their bank account, it is wages.
