It means they pay expenses as a flat amount per day rather than making you submit receipts to substantiate.
Per diem is exempt from income and social security tax. Contractors can realize significant tax savings by having a portion of their wages paid as per diem rather than ordinary taxable income. The employer saves money because he does not pay employer's FICA on the per diem portion. IRS has a schedule of allowable per diem per city. It ranges from $100 per day to over $200 per day in NYC, Chicago, San Fran, and other high cost cities. That's $70K in tax-exempt income. which can reduce taxes by up to $15K. To qualify, you must maintain a permanent home and not stay in the temporary city longer than one year. You must be a W-2 employee, not 1099.