Treasurer Josh Frydenberg says JobKeeper "had to end" to revitalise the economy but financial help for struggling businesses would continue.
The economic lifeline formally ended yesterday, finishing 12 months of financial assistance to retain the links between employers and employees hurt most by COVID-19 restrictions.
Mr Frydenberg told Today that retaining JobKeeper would hurt employment prospects by stopping workers moving to more productive roles.
"Advice from Treasury is that it would be counterproductive for the economy to leave in place JobKeeper as the economy strengthens.
"It would prevent workers moving across the economy to more productive roles. We need to bring it to an end."
At its peak, more than 3.5 million Australians were receiving JobKeeper which was paid to eligible employers to supplement or wholly replace weekly wages.
Mr Frydenberg said targeted government economic help would continue for businesses such as tourism that had been heavily reliant on JobKeeper.
"We've announced more than a quarter of a billion dollars in direct support for travel agents. We also announced a broader package with half-price air fares to destinations across the country. That is designed to get more planes in the air and more tourists on the ground."
Many believe the JobKeeper payment prevented the unemployment rate by blowing out to double figures during the peak of the crisis, by keeping workers employed even when their sectors where largely shut down by restrictions.
At its peak, Australia's unemployment rate only hit 7.68 per cent. It is estimated that JobKeeper in total cost the Australian taxpayer around $90 billion.