Post/Pre tax split of STD Plan

[amxgrlwi]

An employer has a group short-term disability plan that is set up to be partially paid by the employer with remaining premiums paid as pre-tax contributions from employees. However, because of a LOA due to injury that resulted in STD payments, an employee made ONLY post-tax contributions to the plan. The employer drafted the W-2 showing all STD benefits as taxable, with the reasoning that it is a pre-tax group plan, even though this particular employee made all contributions post-tax. The employer has offered to refund the premiums, but I'm not sure if this would abide by IRS regulation.

Should the benefits be taxable or non-taxable in this unique situation?