If your Strata is registered for GST then everyone should have GST charged on the levies. If the Strata is not registered for GST then no one should have GST charged on the levies. You can not simply pick and choose who gets charged GST and who does not. Certain items under the GST Act do not attract GST however Strata Levies are not part of this.
The GST is collected by the owners by the Strata Management on behalf of the ATO and then each month/quarter/ or annually is paid to the Tax Office. This is also reported on the Business Activity Statements the ATO sends out.
The simplest way to see if your Strata is registered for GST is to go to:
It is a government website that lists all entities with ABN (Australian Business Numbers) and the GST registration. If the Strata is or was registered for GST then the Strata should have an ABN.
As for the ATO coming down hard. I will be honest – in my dealings (as a tax accountant) with the ATO there is absolutely no consistency with the way they deal with issues and fines and penalties. The main issue would be if your Strata is over the threshold to be registered for GST and is not on charging GST. However since Strata’s only need to lodge income tax returns for non-mutual income such as interest earned on money sitting in a bank account the chance of the ATO finding out is remote. They have bigger fish to fry.
I would first look at the website and see if the Strata is registered for GST. Your Strata then will need to determine whether they need to be registered. If they are sure they are under the threshold then they do not need to be registered.
Get the GST sorted and it should sort out the one payment issues. 