Per Diem for 2012 is $59 per day, times 80%. If you can claim 250 days, that is $14,750 X .80 = $11,800 deduction. If your company paid you $10,000 for Per Diem, you would subtract that from the deducible amount, leaving $1,800 for a deduction. If your company overpaid you for Per Diem, only the amount above your deduction would be counted as income and taxable.