Tax officials have written to 8000 businesses that are believed to have claimed the JobKeeper wage subsidy despite not being eligible.
The Australian Taxation Office is seeking further information from the businesses to verify their eligibility.
"We are unable to pay businesses that do not meet the requirements of the law," an ATO spokeswoman said.
"If a business owner believes they meet the entitlement criteria, they should phone the ATO.
"The ATO will work with business owners to avoid and overcome honest mistakes, and we will be reasonable and flexible where there have been honest mistakes."
Before contacting the businesses, the ATO looked at income tax returns or activity statements to see if they were undertaking business on March 1 and had an ABN on March 12.
CPA Australia, along with other professional accounting bodies, said the ATO had a huge task to implement all of the stimulus measures but the short time frames and complexity meant that some businesses may not have understood the eligibility rules.
"CPA Australia supports the ATO's approach, however we are seeking further clarity on the (tax) commissioner's ability to waive certain repayments," the body said in a statement.
The organisation has sought changes to the rules to allow new businesses to be considered eligible for JobKeeper payments while also producing guides for its members highlighting the rules around eligibility.
Labor frontbencher Brendan O'Connor said the government was providing inconsistent advice on JobKeeper - something the opposition warned about in April.
"Accountant vouchers would help small businesses with serious cash flow issues access professional advice," he said.
The Morrison government is yet to reveal plans for JobKeeper and the boosted JobSeeker payment beyond their September end date. Several sectors have called for the support to be extended.
Changes are expected to be outlined in an economic statement on July 23.
Following concerns being raised about another stimulus plan - the HomeBuilder scheme - Prime Minister Scott Morrison said the government would be flexible with the grants if there were delays at the state level.
Under the scheme, contracts must be signed by December 31 and construction must commence within three months of the contract date.
"If there are any delays that occur because of planning processes at the state level for people's homes, then we've given the flexibility to the states to continue to provide those grants," he told Sounds of the Mountain radio.
"To ensure that they're not disadvantaged because building in a bushfire zone has some new rules and controls, so people won't miss out on that."
All states and territories have signed national partnership agreements to deliver HomeBuilder, but each is implementing its own grant application processes and payments.
More than 37,000 Australians have registered their interest in the program.
Australian Associated Press