Crossbench members have been told they would only be able to employ one adviser as part of their staffing allocation in the new parliamentary term.
Under the previous coalition government, crossbench MPs and senators were allowed to have two advisers and two assistant advisers.
Newly elected independent Senator David Pocock said the move was bad for democracy and transparency.
"This decision by the prime minister is extremely disappointing and damaging to the relationship with the crossbench," he said in a statement on Friday.
"Cutting three quarters of our parliamentary staffing resource removes transparency, hinders the democratic process and reduces our ability to participate fully in parliament."
A spokesman for One Nation leader Pauline Hanson said her office was working alongside other crossbench MPs to retain the previous allocation of staffing.
"It's in the interests of the Australian people that Senator Hanson and others on the crossbench have staff numbers sufficient to properly scrutinise and improve legislation," the spokesman told AAP.
A Labor spokeswoman said staffing numbers were reviewed and reallocated after every election.
"In recognition of the enlarged crossbench, the government intends to increase resources of the parliamentary library which all parliamentarians can use for information, advice, research and analysis of legislation," the spokeswoman said.
The new parliament, which will sit from late July, will have 12 independent or minor party MPs in the House of Representatives, while there will be six in the Senate.
Senator Pocock said adequate staffing resources were needed in order for the government to properly be held to account during the next term.
"Consulting with my fellow crossbenchers, we have shared concerns about voting on legislation we don't have the resources to adequately scrutinise or ensure the integrity of," he said.
"This decision is bad for democracy and terrible for transparency, parliament should represent all Australians."
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