The scam involved people acquiring an Australian Business Number before registering a fictitious business via their MyGov account.
Fraudsters would then submit a fake business activity statement, claiming they had spent a huge amount of money to set up the company, before applying for a 10 per cent GST refund from the tax office.
The ATO launched Operation Protego in April last year to pursue the fraud, which led to a series of raids across Melbourne, Sydney and Brisbane.
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Federal police arrests have since led to the convictions of 10 fraudsters, with compliance action taken against more than 56,000 thousand people.
The ATO said it has prevented another $2.7 billion in attempted fraud.