How can I justify using a cost reimbursement contract for the purchase of commercial items required for service contract completion?
I am assuming that the basic service your office is procuring does not meet the definition of a commercial item at FAR 2.101. If that's the case, then a service does not become a commercial item simply because it involves the purchase of some services and parts that could be considered commercial items. The vast majority of (if not all) non-commercial services contracts require some supplies and services for contract performance that meet the FAR definition of a commercial item. For example, a fighter aircraft (not a commercial item) requires some avionics components that are shared with commercial aircraft.
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If the primary objectives of the work statement do not conform to the definition of a commercial item, the contracting officer should have no problem documenting the contract file with the rationale for using a cost-reimbursement type contract.