Scott Morrison says he drew upon his "own experience and understanding" in dismissing Treasury's expert advice on negative gearing.
The ABC last month revealed the Treasury told Mr Morrison that Labor's housing taxation overhaul would probably have a "small" impact on prices.
Despite receiving the advice in early 2016, Mr Morrison went on to claim the policy would be a "sledgehammer" to the market.
"I didn't agree with them," Mr Morrison said on Tuesday.
"I take advice from my officials but I'll make my own decisions based on my experience and based on consulting widely.
"Treasury's advice is their advice, but it wasn't based on any economic modelling."
Mr Morrison pointed to his experience as a "research economist in the property sector".
He worked for the Property Council — a group that strongly opposes the ALP policy — in the late 1980s and early 1990s
Documents predicted 'small' price changes from ALP policy
The previously confidential documents, released under Freedom of Information laws, predicted that "price changes [were] likely to be small".
"The ALP policies could introduce some downward pressure on property prices in the short term," the Treasury advice said.
"In the long term, increases in taxation on rental property could have a relatively modest downward impact on property prices."
Ministers variously claimed the plan would "destroy" home values and bring the economy to a "shuddering halt".
Labor said the documents proved that ministers had lied to Australians for two years.
"They were just engaging in a political smear and scare campaign, they knew it wasn't backed by the facts," shadow treasurer Chris Bowen said in January.
Mr Morrison said the Government's moves to restrict investor lending had slowed price growth "from 17 per cent in Sydney to down to just over 1 per cent".
"You've got more first home buyers in the market, house price growth has decelerated and is back now at a more sustainable level," he said.
"So what's the point of Labor's negative gearing policy?
"What Labor proposes would be damaging to the interests of the Australian economy, and particularly at time when we're in resurgence, I think this puts all of that at great risk like their other tax hikes."
Labor has proposed restricting negative gearing to new homes from July 2017, and to halve the CGT discount.
It would grandfather existing investments.
Despite snubbing its advice, Mr Morrison said he respected the work of his department.
"They're a fantastic organisation," he said.