Mr Macron told Australian journalists on the sidelines of the G20 summit in Rome "I don't think, I know" the Australian prime minister lied to him.
"I have a lot of respect and a lot of friendship for your people," Mr Macron said.
"I just say when we have respect, you have to be true and you have to behave in line and consistently with this value."
Mr Morrison did not agreed with suggestions he lied to the French president.
"No," the prime minister told reporters in Rome when asked if Mr Macron's claim was true.
He added he would "always stand up for Australia's interests."
Mr Morrison maintained Australia was in the process of repairing its relationship with France.
"We've begun it, we've spoken several times over the last couple of days. I'm sure we'll speak a bit more before I head back to Australia," he said.
Australia in September announced it was cancelling its 2016 contract to acquire conventional Attack Class submarines from French company Naval Group.
Instead, the government will spend 18 months looking at the feasibility of acquiring technology for nuclear-powered vessels from the US and UK.
The shock AUKUS announcement was kept under tight wraps and infuriated France, which responded by temporarily recalling its ambassadors from Australia and the US.
Treasurer Josh Frydenberg defended Australia's actions as necessary to protect its strategic interests.
"He's (Scott Morrison has) made very clear that he hasn't (lied)," Mr Frydenberg told the Nine Network on Monday.
He separately told reporters he understood France's deep disappointment.
"It's a difficult time in the bilateral relationship. There's no secret in that. But at the same time, we are looking for opportunities to rebuild it," the treasurer said from from Melbourne.
"The AUKUS relationship is a groundbreaking one and a very significant moment, I think, for Australia's national security posture."
Meanwhile, Acting Prime Minister Barnaby Joyce wanted everyone to move on from the submarine issue.
"We didn't steal an island, we didn't deface the Eiffel Tower. It was a contract," he told media from Moree in northern NSW.
"I hope that President Macron understands that, ultimately, Australia and France have got so much more in common and so much into the future than a contract which is now in the past."
Agriculture Minister David Littleproud thought Mr Macron's ire had more to do with the upcoming French presidential election than the contract.
"It's unreasonable. The prime minister had dinner with the president in June and made it clear the subs we were purchasing wouldn't meet our strategic needs into the future," he told the Nine Network.
US President Joe Biden conceded to Mr Macron the way the decision had been handled was "clumsy" and "not done with a lot of grace".
"I was under the impression certain things had happened that hadn't happened," Mr Biden said.
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