Can a taxable Fringe Benefit be added to a W2 if it hasn't been run through payroll?

We just found out a company we do payroll for has been paying for a hotel room 4 nights a week for an employee that lives 200 miles from the main office for the entire year.  Is there a way to add this to the W2 since the taxable amount was not run through payroll, or should this be reported on a different form?