Mr Morrison said the shortfall in the cost was similar to a housing contractor originally quoting $350,000 to build a new home, but the ultimate bill being $250,000.
“That is news that you would welcome,” he said.
The Prime Minister said JobKeeper was created and estimates about its spread made by Treasury at a time of “incredible uncertainty”.
He said ultimate responsibility for the program rested with him.
Mr Morrison said future taxpayers would be better off because JobKeeper, funded with borrowed money, would not cost as much.
“What it means is that Australians won’t have to borrow as much money,” he said. “It’s not going to cost Australia more money, it’s going to end up costing Australians less.”
While saying there appeared to be far fewer people on JobKeeper than originally estimated, Mr Morrison revealed there was an “elevated” number of people on JobSeeker.
He said there had been a four-fold increase in the number of Australians accessing social services support.
Labor is demanding Treasurer Josh Frydenberg face the Senate committee created to oversee the government’s spending on the pandemic.
Its finance spokeswoman Katy Gallagher said Mr Frydenberg, who had claimed credit for the size and scope of the government’s response to the coronavirus, needed to be upfront about what went wrong with the JobKeeper estimates.
“The $60 billion bungle is also unprecedented and the Treasurer is the architect of that,” she said.
“It goes straight to the heart of his credibility and competence and I would have thought he would have welcomed an opportunity where he is given the opportunity and a platform to explain what went wrong and what the government is doing about it.
“When you think about it, ministerial statements have been incorrect, speeches in the Parliament have been incorrect, evidence before the committee has been incorrect. This has been going on for eight weeks now.”
Mr Morrison said when the committee was created, Labor understood it could not call ministers who sit in the House of Representatives such as Mr Frydenberg.
Shane is a senior economics correspondent for The Age and The Sydney Morning Herald.