If you determine in advance of the employee's travel that payment from a non-Federal source will cover some but not all of the employee's allowable travel and subsistence expenses you should state on the employee's travel authorization that the employee will be reimbursed the difference between the full allowances and the payment from the non-Federal source. See chapter 301 of this Title, 6 Foreign Affairs Manual, Chapter 100, or the Joint Travel Regulations (JTR), Chapter 4, as applicable to determine the applicable maximum allowances.
41 C.F.R. §304-6.2