CRA states that it may not abide by provincial garnishment limitations except in Quebec

When a trade receivable of $100 plus $13 of HST owing to a tax debtor is garnished by CRA to satisfy part of the $200 tax debt of the tax debtor to CRA, this very well may mean that the tax debtor will not have the funds to satisfy its obligation to remit the $13 with its monthly HST return. CRA noted that this may not have an adverse arrears interest effect on the tax debtor because, although it will be accruing more interest on its current unpaid remittance, the old tax debt has been reduced.

CRA indicated that it no longer respects provincial garnishment limitations (apparently for ITA purposes as well as GST/HST purposes) except that it abides by the Quebec limitations respecting GST collections in Quebec to stay coordinated with the ARQ, which is legally bound by the Quebec limitations. Examples of where CRA may exceed the provincial limits in the Rest of Canada include situations

where there were other sources of income and only one income source was to be subjected to garnishment action, assets that could be readily available to the debtor to generate funds to satisfy the tax debt in full or a substantial portion and the debtor was not cooperating, or situations where the provincial exemption amount would be insufficient to address the amount of arrears.

Neal Armstrong. Summary of 25 February 2016 CBA Roundtable, Q. 4 under ETA s.317.