Speaking at a campaign-style event, Harper said Canadians across the country have owned guns for years for security and other purposes without resorting to vigilantism.
"That's just not the reality of this situation," the prime minister said at a factory just west of Toronto.
"Gun owners in Canada are not allowed to take the law into their own hands. Nobody here is suggesting they should be able to do that."
Harper denounced his critics as confused rabble rousers who don't like gun owners.
"People misunderstand the difference between our system in Canada and the system in the United States," Harper said.
"Gun ownership in Canada is a responsibility, unlike the United States (where) gun ownership is a right."
No one, he said, has proposed going to the American system.
The prime minister's comments came after Opposition Leader Tom Mulcair and other critics pounced on remarks he made recently in Saskatchewan in which he talked about gun ownership in rural areas.
People who don't live close to police stations or immediate assistance from officers keep guns for a "certain level of security," Harper said.
In Vancouver Wednesday, Mulcair called the comments "bizarre" and "disquieting" but said Harper appeared to be changing his tune.
"I'm happy to see that the prime minister is now backing away from what was an incredibly ill-considered statement," Mulcair said.
Jenni Byrne, the national campaign manager for the Conservative party, added fuel to the issue when she used Harper's Saskatchewan comments as a fundraising tool.
In an open email to potential donors, Byrne said the party recognizes that guns play an important role in the "safety of many Canadians."
She also took a dig at both Mulcair and Liberal Leader Justin Trudeau.
"They want to make life harder for lawful hunters, farmers, and sport shooters by bringing back the long-gun registry," Byrne said.
"At the same time, they oppose everything we do to punish criminals who commit crimes with guns."
Quebec Premier Philippe Couillard also weighed in, saying Canadians don't want to live in a country with an "abundance of firearms," while Ontario's former attorney general, Michael Bryant, condemned Harper's remarks.
The prime minister, Bryant told the Ottawa Citizen, "misstated" the truth about domestic law by linking gun ownership with the right of rural Canadians to use firearms for their own safety.
"It’s not Canadian law," Bryant said. "It's vigilantism. People are going to find themselves facing the criminal justice system and being charged with serious crimes if they decide to follow what the prime minister is suggesting."
On Wednesday, Harper rejected that view.
Canadians who want to own a gun have to accept a "range of responsibilities" that include obtaining a permit and respecting the law, he said.
"We have a law-abiding gun community in this country," he said.
He painted the opposition parties as "clearly anti-gun owners," unlike the Conservatives who have scrapped the "needless and ineffective" long-run registry.