FROM CFIA
Canadian Goods returning to Canada, regulated and classified between chapter 1 and 97
AIRS have an end use option of 'Canadian goods returning' which should be selected for these products. For EDI, the AIRS tool will require the Importer/Broker to declare the 'Country of Origin' as the country from which the goods are being sent and select the end use of "Canadian goods returning" in order to identify the proper import requirements.
Note: AIRS is designed for the purpose of import so there is no option for Canada as a 'country of origin' available in the AIRS tool.
 
For example:   A Canadian good has gone across the border into New York, US and is being shipped  back to Canada. In this case, the origin submitted to CBSA is Canada. CFIA will require that US (New York) be declared as the Country of Origin, and the end code of "Canadian Goods Returning" selected in AIRS tool. Both data elements for the Country of Origin (CBSA and CFIA) will be required in order to receive an EDI release.
 
Reasoning: There may be potential risk associated with different geographical regions/countries. In order to control the risk, AIRS is structured to work by identifying risk associated with different geographical regions/countries for any given commodity which CFIA regulates.
 
Canadian Good returning classified under headings 9813 and 9814,
CFIA regulated goods declared under chapter 98 must be submitted using paper. Transaction(s) will be rejected if EDI is used. Brokers have been advised that until further notice they are to select the "OGD requirement" box on the CBSA exception lead sheet for CFIA regulated commodities declared in headings 9813 and 9814 as there is not enough information for CFIA to make an electronic release decision using these HS headings.

The CSCB followed up with CBSA, asking if showing an incorrect origin for CFIA purposes would result in non-compliance. Their response was:
 
If the broker chooses to use EDI to obtain release of “Canadian Goods Returned” (CGR) and the goods are regulated by CFIA, they would need to classify the goods under the applicable chapter (1-97) and then when they file their final accounting would specify the appropriate CGR tariff and Canada as country of origin.  This is to confirm that the information on the final accounting documentation would be changed so that the importer may then benefit from the CGR duty/tax assessment.  Difference in this information between the interim accounting and final accounting would not be considered inaccurate data by the CBSA since current provisions allow for this “way around” which supports EDI without compromising the importer’s entitlement for relief under CGR tariff.