The federal government has flagged some GST relief for Australians affected by a new 30 per cent tax on discretionary trusts, which kicks in from July 2028.
But Labor has stopped short of guaranteeing a reprieve on stamp duty, which thousands of people will likely need to pay as they restructure their investments as a result of the changes.
The reforms outlined in the budget attempt to even the tax rates on wages and investments, but businesses claim they will lead to a "double whammy" of taxes which could stifle innovation.
The states had a crucial role to play in helping ease the transition to the new tax system, Chartered Public Accountants Australia tax lead Jenny Wong said.
"Whilst there is the proposed three-year rollover relief from income tax to restructure out of a discretionary trust structure, its effectiveness will depend heavily on whether state and territory governments provide corresponding stamp-duty relief," she said in a statement to AAP.
"Without co-ordinated duty concessions, many small businesses and family groups could still face significant transaction costs when restructuring out of discretionary trusts, potentially undermining the practical benefit of the rollover measures."
Hundreds of thousands of small businesses are believed to rely on discretionary trusts, which allow owners to split income across family members to minimise tax, while helping to shield assets from disputes.
Businesses would be slugged twice under the changes: first by changing their trust structure and then having to pay stamp duty, Australian Chamber of Commerce and Industry chief executive David Alexander said.
"Paying stamp duty on top of being effectively forced into a higher tax structure would be a double whammy for small and medium businesses, when no whammy at all is justified," he said.
"Restructuring from trusts to a corporate structure would also entail considerable costs through accounting and financial advice."
While the first big reforms from the budget will be introduced into parliament in coming weeks, the overhaul of trusts won't be included in that tranche of legislation, Prime Minister Anthony Albanese said on Tuesday.
"The trust changes will take longer to develop, but we'll be introducing that legislation this year as well," he told reporters in Perth.
Asked whether stamp duty relief was being considered, Mr Albanese said it was a matter for the states.
"We will work through with state governments those issues. They are state taxes, not commonwealth taxes," he said.
The tax changes, along with measures paring back negative gearing investments, will need the support of the Greens to go through parliament, with the coalition promising to fight the policies and repeal them if it wins government.
Small business owners were "under assault" from the changes to trusts, Opposition Leader Angus Taylor declared.
"The Labor Party clearly doesn't like small business and they want small businesses to help fund their rapid growth in spending," he said.
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