There is disclosed a method and system for automatically processing of shortage deduction transactions utilizing Radio Frequency Identification (RFID) for goods sold. A shortage deduction takes place, in connection with transactions involving one selling company and one buying company, when the buying company remits less than the pre-agreed rate citing reasons related to shipping or transportation issues for withholding part or all of the payment. The processing may include data matching and proactively tracing invoice transactions that are identified as shortage upon comparing the Electronic Product Code (EPC) information. If mismatch occurs during transportation a claim is filed with the freight company. If mismatch occurs after goods are received at the retailer's store(s) a declination will be issued. Deductions are also declined when EPC comparisons made on shipments that the deductions reference do not result in mismatch.