According to the Canada Revenue Agency's RC4022: General Information for GST / HST Registrants there are no GST late filing penalties if your GST/HST account has a $0 balance or the Canada Revenue Agency (CRA) owes you a refund on your GST return.
However, if that's not the case and you file a late return, the GST penalties are 1% of the amount owing plus the result of the following calculation:
25% of the amount you calculated in (a) above × the number of months the return is overdue, to a maximum of 12 months.
But that's not all. The Canada Revenue Agency will also charge interest on an overdue amount equal to the basic rate plus 4%.
Late filing of a GST return is not the only way you can incur GST penalties. You can also be fined for non-compliance. If you receive a demand to file a return and do not do so, a penalty of $250 will be charged.
And just to rub some salt into the wound, you can't claim any income tax deduction for any penalty you paid or owe for failing to file a GST/HST return or for any arrears interest you paid or owe for outstanding GST/HST amounts.
The moral of the story is you definitely want to get your GST / HST return in on time if you owe the CRA money.
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