Common GST/HST Filing Errors
and Solutions: Troubleshooting
GST/HST errors are among the most common — and most expensive — compliance mistakes Canadian businesses make. Wrong provincial rates, unclaimed input tax credits, late filing penalties, incorrect place-of-supply determinations, and missed registration deadlines collectively cost Canadian businesses tens of millions in avoidable penalties and lost ITC refunds every year. This comprehensive troubleshooting guide identifies every major GST/HST filing error category, explains exactly what goes wrong and why, and provides the specific solution for each problem — whether you are fixing past errors or preventing future ones.
1. GST/HST Overview — The Framework Every Business Must Understand
The Goods and Services Tax (GST) and Harmonized Sales Tax (HST) is Canada’s federal consumption tax. The GST rate is 5%. In provinces that have harmonized their provincial sales tax with the federal GST, the combined HST rate is higher: Ontario 13%, New Brunswick/Nova Scotia/Newfoundland & Labrador/PEI 15%. Saskatchewan, Alberta, Manitoba, British Columbia, and Quebec have not harmonized — businesses in these provinces charge 5% federal GST separately from provincial sales tax (PST/QST). Every business generating more than $30,000 in taxable supplies in any calendar quarter or four consecutive calendar quarters must register for GST/HST and file periodic returns.
For mobile app and software businesses where GST/HST on digital services creates specific complexity, our Mobile App Business Plan guide covers the sector-specific context. Automotive businesses should see our Automotive Business Tax Planning guide. Startups setting up GST/HST for the first time should review our Complete Fractional CFO Services for Startups guide. First-time business owners should read our First-Time Business Owner Tax Compliance guide. Saskatchewan businesses with PST in addition to GST should see our Business Name Registration guide. For documenting business expenses that generate ITCs, our Documenting Business Expenses guide is essential. Tourism businesses with complex GST/HST treatment should see our Tourism Business Plan guide. And e-commerce businesses selling digital products should review our E-Commerce Tax Planning guide.
📋 Are You Making GST/HST Errors That Are Costing You Money or Creating CRA Risk?
Custom CPA reviews your GST/HST filing history, identifies errors and unclaimed ITCs, and implements the compliance system that eliminates filing errors and maximizes legitimate ITC recovery.
2. Error: Wrong GST/HST Rate Applied
What goes wrong: a Saskatchewan business charges every customer 5% GST — including customers in Ontario who should be charged 13% HST. An Ontario business charges 13% HST to an Alberta customer who should pay only 5% GST. An online retailer uses a flat 5% GST on all Canadian sales regardless of delivery province.
Why it happens: the place-of-supply rules are not intuitive. The applicable rate is determined by where the goods are delivered or where the service is received — not where the seller is located. Businesses that sell to customers across multiple provinces must apply the destination province’s HST rate — a task that requires either manual rate management or a properly configured e-commerce or invoicing platform.
The financial consequence: undercharging the correct rate: the seller owes the correct amount to CRA regardless of what they charged the customer. A seller who charged 5% GST to an Ontario customer but owed 13% HST must pay the 8% shortfall from their own funds. Overcharging: charging an Alberta customer 13% HST when only 5% GST was required; the seller must refund the 8% excess to the customer or apply for an adjustment.
3. Error: Missed or Unclaimed Input Tax Credits
What goes wrong: GST/HST paid on business expenses is a refundable credit — but only if it is actively claimed on the GST/HST return. Many businesses consistently under-claim ITCs because: receipts are not coded as GST-paid in the accounting software; the bookkeeper is not aware of ITC eligibility rules; mixed personal/business expenses are excluded entirely rather than partially claimed; or the business is unaware that certain categories of expense are ITC-eligible.
4. Error: Charging GST/HST on Exempt Supplies
What goes wrong: a business collects GST/HST from customers on supplies that are exempt under the Excise Tax Act. The collected amount must be remitted to CRA — but the customer who paid the exempt supply’s “HST” was not legally required to pay it, creating a potential refund obligation.
| Exempt Supply Category | Why Commonly Confused | Correct Treatment |
|---|---|---|
| Long-term residential rental (30+ days) | Landlords sometimes charge GST on residential rent, believing all rent is taxable | Exempt — no GST charged; no ITCs on inputs used exclusively for residential rental |
| Medical services (physicians, dentists, optometrists) | Practices sometimes charge HST on services before confirming exemption | Exempt — physician and dental services are exempt under ETA Schedule V, Part II |
| Psychological services | Confusion between registered psychologists (exempt) and unregulated counsellors (taxable) | Registered psychologist services: exempt. Unregulated counsellors: taxable. |
| Registered psychotherapy in Ontario (post-Oct 2024) | RPs who were collecting HST before the 2024 exemption may not have updated their billing | Exempt from October 2024 onward for Ontario RPs. Stop collecting HST on psychotherapy. |
| Financial services (interest, insurance premiums) | Some businesses charge HST on financial service fees that are specifically exempt | Financial services as defined in ETA are exempt. Confirm category with CPA. |
| Basic groceries | Food retailers sometimes apply GST to zero-rated grocery items | Zero-rated (0% GST) for most food for human consumption. Prepared food and restaurant meals are taxable. |
5. Error: Late Filing and Late Remittance
The penalty cascade: GST/HST deadlines are unforgiving. Missing the filing deadline — even by one day — triggers automatic penalty assessment if there is an amount owing. Missing the payment deadline triggers immediate interest at compound daily rates. Director personal liability means the consequences extend beyond the corporation.
6. Error: Incorrect Place of Supply Determination
The rules in plain language: for most supplies, the applicable GST/HST rate is determined by where the supply is made — the destination province, not the seller’s province. This affects every business that sells to customers in multiple Canadian provinces.
| Supply Type | Place of Supply Rule | Common Error |
|---|---|---|
| Physical goods shipped to customer | Province where goods are delivered to the customer | Seller charges their home province rate regardless of delivery destination |
| Services (most types) | Province where the service is primarily performed | Charging HST on services performed in an HST province for a customer in a non-HST province |
| Digital products (ebooks, software, subscriptions) | Province of the recipient’s billing address or residence | Applying a flat 5% GST to all digital sales regardless of customer location |
| Real property services (construction, renovation) | Province where the real property is located | Charging home province rate for work performed at a property in another province |
| Intangible personal property (IP licenses, software rights) | Province of use by the recipient | Applying seller’s province rate to IP licensed for use in a higher-HST province |
7. Error: Failing to Register When Required
What goes wrong: a business crosses the $30,000 taxable revenue threshold — either in a single quarter or cumulatively over 4 quarters — and continues operating without registering. The business collects no GST, claims no ITCs, and files no returns. CRA identifies the gap through T2 income cross-referencing, payment processor data, or industry targeting audits.
The retroactive assessment: CRA can assess GST/HST retroactively from the date the registration obligation arose — plus penalties and compound interest. If a business had $300,000 in taxable Ontario revenue in the 2 years it operated unregistered: retroactive HST = $300,000 × 13% = $39,000 — plus 1% penalty and compound interest. Because the HST was never collected from customers, this $39,000+ comes from the business’s own funds.
8. Error: Misclassifying Zero-Rated and Exempt Supplies
The critical distinction most business owners miss: zero-rated supplies (Schedule VI of the ETA) and exempt supplies (Schedule V) are both non-taxable — but they have completely different ITC treatment.
9. Error: ITC Documentation Failures
What CRA requires to support ITC claims: an ITC claim is only valid if supported by the documentation prescribed by the ETA. The required documentation varies by the amount of the ITC claim. CRA will disallow ITCs in an audit if the documentation requirements are not met — even if the underlying expense was legitimate.
| Purchase Amount | Minimum Documentation Required | Common Failure |
|---|---|---|
| Under $30 | Amount paid; supplier name; GST/HST paid | No receipt at all — claiming ITC from credit card statement with no backup |
| $30 to $149.99 | Supplier name and address; date; amount paid; GST/HST paid or supplier’s GST registration number | Receipt shows amount but not GST breakdown; no registration number |
| $150 and above | All of the above PLUS: purchaser’s name; description of property or service; terms of payment | Receipt is insufficient (no purchaser name); GST not separately identified on the invoice |
| Intercompany / related party transactions | All of the above plus arm’s-length pricing confirmation and business purpose documentation | Related party invoices without proper documentation; non-arm’s-length pricing |
📈 Identify and Fix Every GST/HST Error in Your Filing History — Before CRA Does
Custom CPA conducts a comprehensive GST/HST filing review — checking rates, ITC claims, supply classification, place of supply, and documentation — identifying every error and implementing the corrections before CRA initiates a review.
10. CRA GST/HST Audit Triggers
Understanding what triggers a CRA GST/HST audit allows businesses to proactively review and correct errors before they are identified externally:


