Anthony Albanese told crossbench MPs and senators on Friday the number of parliamentary staff they could hire would be cut from four to one senior adviser, alongside their four electoral office staff.
"They're not totally on their own," he told ABC radio on Monday.
"They have access to the Parliamentary Library that we will be increasing support for, they have access to clerks that draft legislation in addition to personal staff."
There had also been "misconceptions" about the job of electoral office staff, who often did parliamentary work, Mr Albanese said.
But independent ACT senator David Pocock accused the prime minister of making the decision to gain political advantage.
"Cutting back on our small teams creates an unfair playing field which disadvantages our communities and our capacity to actually advocate on their behalf," Senator Pocock told ABC radio.
"It could be incredibly hard to actually be across legislation and if I don't understand things it's going to be very hard to actually vote on them."
Under the previous coalition government, MPs and senators outside a party structure were allocated two advisers and two assistant advisers.
Yet all members of parliament work hard and crossbenchers should not have an unfair allocation of more staff, Finance Minister Katy Gallagher said.
More than $1.5 million would be saved on staffing allocations compared with the previous government through fewer numbers overall, as opposed to shifting resources away from crossbenchers only, Senator Gallagher said.
Independents will still have the four electorate staff all members are allocated, plus one additional parliamentary staff member.
Senator Gallagher says the extra staff member shows the government's commitment to respecting the crossbench and the role they play in parliament.
"They get one additional personnel allocation and we believe that's a fair and sustainable way forward."
Senator Pocock wants the prime minister to reconsider.
"I want to be constructive, to represent a community I love. I'm certainly not going to just vote against things to make a point, that's not how I do things," he said.
Lower house independent Kylea Tink, who won North Sydney from former Liberal MP Trent Zimmerman, is hopeful the prime minister will reconsider his decision upon his return from the NATO meeting in Madrid.
"The prime minister's correspondence made clear the reduction was a proposal, it's not a fait accompli," she told AAP.
"Australians voted for a bigger crossbench because they want to see change and that will only be possible if we are well resourced."
Ms Tink will be one of 35 newly-elected MPs travelling to Canberra this week for their parliamentary induction.
The new members of the crossbench will meet to discuss staffing allocations and assess the other resources available before making a case to the prime minister, she said.
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