Welcome to the Community! It's great to see that you're using QuickBooks Online to manage your business. I can help point you in the right direction.
QuickBooks Online includes several different sales tax related reports to help you review and track your GST such as:
GST/HST Detail Report
GST/HST Exception Report
GST/HST Summary Report
Taxable Sales Summary
Transaction Detail by Tax Code
Transactions without sales tax
I'm not sure which report you're referring to when you mention the sales tax report, but the first thing I recommend doing is confirming that both reports are using the same date range, as if the date ranges aren't matching there'll be differences in the data displayed. You'll also want to ensure that both reports are using the same accounting basis, as that can cause differences in the report data as well. Unless given permission from the CRA to report using cash basis, you'll run your reports using the accrual basis of accounting.
If you're still having issues determining the cause of the difference, checking with an accountant can help you determine what's going on. You can invite your accountant to view your QuickBooks Online company through the My Accountant tab. If you're not currently working with an accountant, you can use the Find a pro to help option to search for a QuickBooks certified Pro Advisor in your area who can assist you.
Please feel free to elaborate further on what reports you're using so that I can help you get to the bottom of this. I'm here to help!
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