DEFINITION of 'Per Diem Payments'. Generally, a specified amount that employers will pay to employees as reimbursement for various expenses. Per diem payments usually assume a set dollar limit, such as $30 per day for meals or $100 per day for lodging. These payments are usually made for employee travel expenses.er diem payments are usually counted as nontaxable income to employees, up to a certain amount, and any excess reimbursement is included in box 12 of the W-2 form. The IRS allows a preset amount to be excluded from taxation for each type of per diem expense. RELATED TERMS.