He also admitted mistakes in his past dealings with the Aborigines.
Howard has had a strained relationship in the past with the Aboriginal community and critics were cautious of his new push to recognise Australia's indigenous people.
"When a snake sheds his skin, he has a shiny new skin, but he's still the same old snake, with the same old venom"
David Ross, director of the Northern Territory's Central Land Council
"It would seem Mr Howard's actions over 11 years belie his words," David Ross, the director of the Northern Territory's Central Land Council, said.
"When a snake sheds his skin, he has a shiny new skin, but he's still the same old snake, with the same old venom."
The New South Wales Aboriginal Land Council said Howard had failed to understand that Aborigines needed the government to say sorry for past wrongs.
Bev Manton, a council chairwoman, said Howard was launching a last-ditch attempt to rewrite his failed legacy on Aboriginal issues.
"His continued dismissal of an apology demonstrates this is all about John Howard in the anticipated dying days of his prime ministership, rather than any genuine attempt to reconcile this nation," she said.
Even Aboriginal leaders who accepted as genuine the motives behind Howard's referendum proposal said he was wrong to continue to rule out saying sorry.
But Howard said an apology involved "shame and repudiation" of Australia's past and would only blame the current generation for the mistakes of their forebears.
He said his proposal allowed reconciliation to take place in a positive way.
"I think to typify this as to whether you do or don't say sorry is to misunderstand what is involved and to trivialise it," he told reporters.
The Aborigines have a number of historical grievances with the Australian government, including the seizure of Aboriginal children which went on until the 1970s.