It's not entirely clear to me that a chaplain can even have a housing allowance. The answer is yes if you work for your denomination and are assigned to the hospital by your denomination. (For example, you are a Catholic priest and your bishop assigns you to work at the hospital.) However, if you are an employee of the hospital, I am not sure you can legally have a housing allowance. This would require more research, and you may need to discuss with an accountant who specializes in clergy tax issues. (yes, they are rare, but you might find one by asking local churches who they use.)
In any event, if your W-2 box 1 salary is reported as $28,000, but is supposed to be a $25,000 housing allowance, then your W-2 is wrong. There is no way to fix this on your tax return that won't trigger an angry letter from the IRS. You need a corrected W-2 from the employer.
If the employer refuses to issue a corrected W-2, you can file using form 4852 "substitute W-2." You would report $3000 in box 1 and all other numbers the same. ($3000 also in box 16, unless you live in a state without income tax--leave it blank--or you live in a state that taxes your housing allowance--enter $28,000.). Then enter the housing allowance separately--remember this is still subject to self-employment tax. But you should give the employer a fair chance to correct the W-2, and keep your correspondence, because using form 4852 may trigger a letter from the IRS. Don't send documents or explanations when you file, but keep all your documents in case of getting that letter.
Also remember that boxes 3-6 should be blank, if you have social security and medicare withholding, then your employer is taxing you wrong in that area as well, and you need to make further adjustments on your tax return.
