I would have to know what area on the W2 your employer is reporting the benefit on. In some cases, the employer can report the health insurance as "income" if he is paying the money to you and then you are buying the insurance out of your pocket. However, I don't otherwise see how he could be reporting it as income. It is still deductible to him as an expense no matter how he reports it on your W2. In any event, you may need to talk to your accountant as to how to correctly get it reported on your tax return even though it is wrongly reported on your W2 if your employer wont change it. If it is a large employer, it may simply be a matter of dealing with the bureaucratic process.
Is your employer aware that you claim your domestic partner as your dependent for tax purposes? If not, then your employer is probably doing the safe thing and treating your domestic partner as a non-dependent. To change this, you should speak with your employer's HR department.
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