At the moment QuickBooks Online is unable to support Fuel Tax Credit (FTC) calculation in the current offerings. You'll have to manually calculate and enter the amount on file. Furthermore, you have the option to turn on the FTC in the GST Settings of QuickBooks Online to record income and show on your BAS. Here's how:
Click on the GST tab.
Click on the Settings button.
Select Tax settings.
Go to Other taxes, and tick box for Fuel Tax Credit.
Click on Save.
Once the Fuel tax credit is enabled, a Fuel Tax Credit Income (FTC) account will be created in to your Chart of Accounts to track all FTC amounts.
To record the FTC amount when lodging BAS:
Click on GST tab.
Click on Prepare BAS for the period to be lodged.
On the Let's include other taxes page, tick I need to include a credit over claim and enter the amount.