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Dear Fintric
Many thanks for your professional input. This is kinda helpful!
This is what I’ve been effectively doing.

My only minor niggle is BAS.
Let’s pretend I have no other invoices in a quarter.
I’ve been doing them as you instructed:

Option A (agent sends me GST on sales)
G1 = G6 = G8 =$1100
G3 = $0
G9 = $100

Option B (agent retains the GST on sales, and transfers to ATO)
G1 = G3 = G5 = $1000
G6 = G9 = $0

It would seem that the BAS method would depend on the agent method. This, to me, is not intuitive, because both options relate to the exact same work done, including GSTs involved. In effect, for option B I’m telling ATO that the work was GST-free (yes it was GST-free for me but the nature of the job was not!). However it seems to be the only way to avoid ATO grabbing the $100 from me when dealing with agent choosing option B.

I guess I’ll do BAS according to above, and if audited, point to the relevant emails.

Incidentally the ATO did reply to my email enquiry, confirming that the agent does have authority to transfer GST on sales to ATO using my ABN, and apparently I can track this in the Business Portal. Also incidentally, when I’ve logged on to Business Portal, I have found no trace of the $100. Anyhow we’ll see.