Mr Frydenberg says he would have to retrospectively change laws in order to make companies repay JobKeeper if they no longer need the support.
"Which is not what I am going to do," he told reporters in Tasmania's north earlier in the week.
"Businesses made decisions to receive JobKeeper and then, as a result, keep staff on, which has helped retain hundreds of thousands of jobs across the community.
"JobKeeper has helped save jobs. That is what it was intended to do."
Treasury expects the number of people relying on the payment in the March quarter to be about 1.1 million. It will end on March 31. More than 3.6 million Australians were on the payment at its peak.
Labor MP Andrew Leigh is campaigning for furniture, electrical and whitegoods retailer Harvey Norman to repay the $22 million it received in JobKeeper, after reporting a 116 per cent rise in first-half earnings.
"They don't need a cent of it," he said.
Australian Council of Trade Unions secretary Sally McManus is backing his call, accusing companies of rorting the system.
"They just believe they are entitled to this money even though they have made profits, even though a whole lot of companies are giving bonuses," she told ABC radio.
Ms McManus has pointed to the government's differing approach to chasing Centrelink recipients for overpayments through the so-called robodebt debacle.
"They have no qualms about requesting and forcing people to pay back Centrelink payments - no problem with that whatsoever," she said.
"Somehow we're all supposed to sit back and say 'oh well that's OK, that's just the rules that apply to big business in this country'.
Financial reporting season has revealed which Australian companies are choosing to pay the money back.
Property group Ingenia Communities will repay $1.7 million of the $5.1 million JobKeeper subsidy it received, after strong revenues from holiday parks.
Bedding and homewares company Adairs has returned $6.1 million of the payment after growth in profit.
Medical company Cochlear will repay $24.6 million.
On the flipside, automotive groups ARB Corporation and AP Eagers won't repay JobKeeper payments, worth $9.8 million and $130 million respectively.