Are you saying that you have a code "W" in box 12 on your W-2? That code is indeed only for HSAs.
If you do indeed have an FSA, please see the following:
Are you making contributions to your FSA through a payroll deduction plan?
If yes, then you don't need to deduct your portion, because it's already being done. Your employer has already removed the amounts deducted from your compensation from Wages listed in box 1 on your W-2.
The IRS says
"Contributions to an FSA
You contribute to your FSA by electing an amount to be voluntarily withheld from your pay by your employer. This is sometimes called a salary reduction agreement. The employer may also contribute to your FSA if specified in the plan.
You don’t pay federal income tax or employment taxes on the salary you contribute or the amounts your employer contributes to the FSA."
See IRS Publication 969.
NOTE that there are no reporting requirements for an FSA. The FSA amount may or may not appear in box 14 of your W-2, but even if you enter it, it will not affect your return.
On the other hand, you MUST enter information about an HSA, so it is critical that you contact your employer and find out which one you have, and get a corrected W-2 if necessary.
