"I think they would have had every reason to know that we had deep and grave concerns that the capability being delivered by the Attack Class submarine was not going to meet our strategic interests and we made very clear that we would be making a decision based on our strategic national interest," he told a press conference in Sydney.
Morrison said it would have been "negligent" to proceed with the deal against intelligence and defence advice and that doing so would be counter to Australia's strategic interests.
"I don't regret the decision to put Australia's national interest first. Never will," he said.
Speaking to Sky News Australia earlier on Sunday, defence minister Peter Dutton said his government had been "upfront, open and honest" with France that it had concerns about the deal, which was over-budget and years behind schedule.
Dutton said he understood the "French upset" but added that "suggestions that the concerns haven't been flagged by the Australian government just defy, frankly, what's on the public record and certainly what was said publicly over a long period of time".
"The government has had those concerns, we've expressed them, and we want to work very closely with the French and we'll continue to do that into the future," he said.
Dutton said he had personally expressed those concerns to his French counterpart, Florence Parly, and highlighted Australia's "need to act in our national interest", which he said was acquiring the nuclear-powered submarines.
"And given the changing circumstances in the Indo-Pacific, not just now but over the coming years, we had to make a decision that was in our national interest and that's exactly what we've done," he added.
Canberra was unable to buy French nuclear-powered vessels because they require charging while the American submarines do not, making only the latter suitable for nuclear-free Australia, Dutton said.
With Australia's new submarine fleet not expected to be operational for decades, Dutton said the country may consider leasing or buying existing submarines from the United States or Britain in the interim.
Australia will get the nuclear-powered submarines as part of a new defence alliance announced with the United States and Britain on Wednesday, in a pact widely seen as aimed at countering the rise of China.