The ATO said the fraud attempts involved individuals inventing fake businesses, lodging fraudulent ABN applications and then submitting fake BAS statements to gain a false GST refund.
It said social media advertising had fuelled the scam and it had already stopped $770 million in payments from being issued.
But it acknowledged that delays were likely.
“We have been working with digital platforms to shut down this advertising and stop further fraudulent attempts,” the ATO said. “Legitimate businesses may face extra steps to receive their refunds as extra controls are put in place.”
Mr Greco said many companies relied on the claims to be processed without hold-ups.
“Many businesses operate with legitimate refunds as a normal occurrence, for example, where they sell predominantly GST-free sales and claim back GST credits on all the supplies they procure in running the business,” he said.
“Then there are businesses that can have a substantial refund when they purchase a large capital outlay that puts them in a GST refund scenario.
“Similarly, timing can produce irregular situations where a business is in a refund situation for some time and then when lumpy sales occur there is a GST liability in the future.
“Also new startups that incur outlays for months or years before there are GST liabilities.”
He said accountants and bookkeepers should intervene to help navigate the extra compliance steps.
“Intermediaries such as BAS or tax agents can assist their clients in proactively managing the process by stepping in to validate returns with the ATO in case their clients' return get caught up in the tighter control,” he said.