FSA contributions should not be reported on Form W-2 Box 12. Per the IRS instructions for Form W2, Code W on Box 12 is to report Employer contributions (including amounts the employee elected to contribute using a section 125 (cafeteria) plan) to your health savings account. If you have an FSA, your employer should correct your Form W2.
If your employer will not correct your Form W2 even after you contact them and request a correction, you can contact the IRS and start a Form W2 complaint. You can call them at 800-829-1040 or set up an appointment to visit an IRS taxpayer assistance center (TAC).
The IRS will send your employer a letter requesting that they issue you a corrected W2 within ten days. they will also send you a letter with information on how to complete Form 4852, Substitute for Form W-2, Wage and Tax Statement. You can use this form in case your employer does not correct it and issue you a corrected W2.
Please reach back if you have additional questions.
