Only if your employer believed that your HSA contributions were not excludible from your income should your employer not have excluded the code W amount from the amount in boxes 1, 3, and 5 of your W-2. If the employer had no reason to believe that the HSA contributions were not excludible from your income and mistakenly did not reduce your box 1, 3 and 5 amounts by the code W amount, contact your employer to obtain a corrected W-2.
Otherwise, you'll need to treat the code W amount as being a personal HSA contribution rather than a contribution made through your employer. In the HSA portion of the interview, on the Let's enter your HSA contributions page, TurboTax will show the code W amount as employer and payroll contributions. Enter this same amount as a contribution that you personally made. Click Continue, then enter in the box for Employer and payroll contributions not reported in box 12 of your W-2 a negative entry to cancel out the amount TurboTax is treating as the employer amount to be reported on Form 8889 line 9. You'll end up with a zero on Form 8889 line 9 and a deduction on Form 1040 line 25. There's a chance that the IRS will question the claiming of a deduction for the code W amount, so be prepared to provide explanation, if need be.
