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I was curious about this topic so I checked the Canada Revenue Agency website and found a good article that explains the issues involving taxes on software:

Imported software is treated differently depending on whether it is considered to be TPP or IPP. Generally, software imports considered to be IPP are not subject to GST. If the recipient of the software is engaged exclusively in commercial activities, there is no requirement to self-assess GST on the intellectual property value of the imported software.

Licensed custom software and software provided electronically is considered IPP. Non-custom software and custom software purchased (as opposed to licensed) is considered to be TPP by Canada Customs and is subject to GST on import.

Based on the above, it appears you do not need to collect GST for sales made to your Canadian customers. However, if you ship a physical product, the customer is responsible for paying GST on the imported item.

IPP = Intangible Personal Property
TPP = Tangible Personal Property
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