Machinery of government changes at Prime Minister Tony Abbott's department have more than doubled to $1.3 million.
And the cost of bringing staff from other departments into the Department of the Prime Minister and Cabinet could still be growing.
An overdue answer to a question on notice just released shows the $1.3 million figure was reached by the end of February.
It is not known whether costs have been incurred since then.
It was revealed on Tuesday the DPMC was set to make a number of its newly arrived staff from other departmental restructures redundant.
A number of them will be senior executives in the indigenous unit where a number of people have arrived from other departments.
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Leader of the Opposition in the Senate Penny Wong said the machinery of government changes hurt Mr Abbott's standing as the self-proclaimed Prime Minister for Indigenous Affairs.
"Once that was done, he delivered a budget that cut half a billion dollars from indigenous programs and took an axe to staff."
A prime minister's office spokeswoman said the claims by Labor were irresponsible and misleading.
"Labor are only interested in scaremongering and not at all interested in ensuring services are delivered within communities and on the ground – where they are needed," she said. "The government has allocated $8.5 billion over the next four years for indigenous affairs through the DPMC portfolio alone."
She said Labor's figure included departmental and administration reductions and did not account for reinvestment.
"The key priority for the Commonwealth government is to ensure results are delivered on the ground - spending more time engaging with communities and developing tailored local solutions designed to achieve results," the spokeswoman said.
The news of the cost of DPMC's machinery of government costs comes as spill and fill processes have been launched in the department because not enough people have volunteered for redundancies.
Community and Public Sector Union deputy national president Alistair Waters said the DPMC seemed to be using spill and fill - where staff reapply for their jobs - too quickly.
"There seems to be a stage missing between calling for expressions of interest for voluntary redundancies and the process of spill and fill," Mr Waters said.
He said more time should be given for people to swap the sack with someone who wants to take a redundancy, otherwise known as voluntary redundancy substitution.
Thirty senior executives in the indigenous unit at DPMC have just found out they will take part in a spill and fill that forces them to stake their claim to stay employed there. Other staff were told they would endure a spill and fill included executive level two employees from the domestic policy division.
Mr Waters said a spill and fill could damage the trust between the staff left behind and their employer.
He said giving staff more detailed information about what the department would look like after the restructure would allow workers to make more confident decisions about voluntary redundancies.
"We'd urge the department to avoid using spill and fill."
The department's average staffing level must be reduced by between 350 and 400 full-time equivalent jobs out of a workforce of 2418 because of the federal budget.