Mr Dutton has revealed he is considering "several" applications from South African farmers who are seeking humanitarian protection in Australia.
The minister hit back at South Africa's foreign minister for suggesting the Australian government had "retracted" Mr Dutton's controversial offer to give "persecuted" white farmers from South Africa "special" consideration for refugee visas.
South Africa Foreign Minister Lindiwe Sisulu had earlier said Prime Minister Malcolm Turnbull and Minister for Foreign Affairs Julie Bishop had made a "retraction" of Mr Dutton's comments.
"We have received a letter from the (Australian ministry of) foreign affairs that indicated that what was said by the minister of home affairs is not the position of the government of Australia," foreign ministry spokesman Ndivhuwo Mabaya told AFP.
On Tuesday, Mr Dutton said he had seen the letter but strongly denied the claim it amounted to a retraction.
"I'm not sure what domestic issues are at play in terms of the politics in South Africa that would bring this comment out but it's not based on any factual statement of anyone within the Australian government," he told Sky News.
Mr Dutton said the government's position was "as I stated it a couple of weeks ago". The minister has not suggested a new visa for white South African farmers but suggested they be considered for existing refugee and humanitarian visas.
"And in fact we're having a look at several now," he said.
Mr Dutton also said at the time that farmers deserved "special attention" because they faced violence and land seizures.
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The South African spokesman said their foreign office had also received an effective retraction from the prime minister, via Australia's ambassador.
"We also had a meeting with the high commissioner [ambassador] who conveyed a message from the prime minister, who said the same thing, to indicate that this is not the view of their government," Mr Mabaya said.
Hours later, a spokesman for Australia's Home Affairs Minister told The Australian that South Africa’s comments did not "accurately reflect" the position of Mr Turnbull or Ms Bishop.
"There was no rebuttal of the words of Minister Dutton," the spokesman said.
A spokeswoman for Ms Bishop told SBS News: "The Prime Minister and the Ministers for Foreign Affairs and Home Affairs have been clear and consistent in reiterating that Australia’s current humanitarian visa program is non-discriminatory, with each application assessed on its merits. The program can accommodate those fearing persecution."
Mr Dutton's original comments did call for "special" consideration under the existing humanitarian program, and the Home Affairs deparment confirmed it was considering "potential resettlement" offers for persecuted minorities.
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Foreign minister Julie Bishop said there were no plans to change the "non-discriminatory" nature of the refugee visa, but said she was "working with the home affairs minister to ascertain if any changes are needed".
Mr Dutton's offer to help settle persecuted farmers in a "civilised country" like Australia drew an angry response from South Africa, kicking off a diplomatic row.
Mr Dutton's comments have found support among conservatives in the parliament. Backbench Liberal Andrew Laming and independent Fraser Anning, once of One Nation, spoke at a march in support of white farmers in Brisbane recently.
Senator Anning told SBS News he would support any move to extend special consideration, describing the violence as an attempted "genocide" of white South Africans.
