The fact that your employer included it in your wages strongly indicates they treat it as a nonaccountable plan and the per diem/mileage should be taxed. If an employer is treating it as an accountable plan, they generally would not include it in your wages.
You can contact your employer to verify. It does not have to be in a letter.
If they treat it as an accountable plan, they would need to issue you a corrected W-2.
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