Last week Mr Abbott's director of policy Dr Mark Roberts allegedly made threats to cut resources for the National Indigenous Education Foundation if the Coalition wins office.
Currently, around $25-billion are spent on black Australians each year.
Minister Macklin wants the Coalition leader to give a guarantee that black money will be safe, if his party forms government.
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The Opposition leader's office says there is no basis for the Government's attack.
"Tony has demonstrated his serious and ongoing commitment towards addressing Indigenous disadvantage in this country and has already announced a number of key policies and initiatives to bring this about," a statement said.
